API tools faq
paste
Advertisement
Guest User

Untitled

a guest
Jul 27th, 2016
86
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 199.34 KB | None | 0 0
raw download clone embed print report
  1. 2016-07-27 23:57:53.400 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython'
  2. 2016-07-27 23:57:53.419 [IPEngineApp] Loading url_file u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython/security/ipcontroller-1c9737c4-68fd-49be-b74e-85d8bdda4c49-engine.json'
  3. 2016-07-27 23:57:53.461 [IPEngineApp] Registering with controller at tcp://45.113.233.138:59195
  4. 2016-07-27 23:57:53.623 [IPEngineApp] Starting to monitor the heartbeat signal from the hub every 5010 ms.
  5. 2016-07-27 23:57:53.634 [IPEngineApp] Using existing profile dir: u'/scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/log/ipython'
  6. 2016-07-27 23:57:53.637 [IPEngineApp] Completed registration with id 1
  7. 2016-07-28 00:14:25.604 [IPEngineApp] WARNING | No heartbeat in the last 5010 ms (1 time(s) in a row).
  8. cat: write error: Broken pipe
  9. cat: write error: Broken pipe
  10. 2016-07-28 00:20:01.180 [IPEngineApp] Exception in apply request:
  11. 
  12. CalledProcessErrorTraceback (most recent call last)
  13. <string> in <module>()
  14.  
  15. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  16.  71 
  17.  72 def __call__(self, *args, **kwargs):
  18. ---> 73 return self.f(*args, **kwargs)
  19.  74 
  20.  75 if not py3compat.PY3:
  21.  
  22. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  23.  179 args = ipython.unzip_args(args)
  24.  180 with _setup_logging(args) as config:
  25. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  26.  182 
  27.  183 @require(alignprep)
  28.  
  29. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  30.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  31.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  32. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  33.  113 data = _add_supplemental_bams(data)
  34.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  35.  
  36. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  37.  62 else:
  38.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  39. ---> 64 names, align_dir, data)
  40.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  41.  66 if not data.get("align_split"):
  42.  
  43. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  44.  115 config = data["config"]
  45.  116 align_fn = TOOLS[aligner].align_fn
  46. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  47.  118 # handle align functions that update the main data dictionary in place
  48.  119 if isinstance(out, dict):
  49.  
  50. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  51.  145 else:
  52.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  53. --> 147 names, rg_info, data)
  54.  148 data["work_bam"] = out_file
  55.  149 return data
  56.  
  57. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  58.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  59.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  60. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  61.  158 return out_file
  62.  159 
  63.  
  64. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  65.  19 try:
  66.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  67. ---> 21 _do_run(cmd, checks, log_stdout)
  68.  22 except:
  69.  23 diagnostics.end_cmd(cmd_id, False)
  70.  
  71. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  72.  93 s.communicate()
  73.  94 s.stdout.close()
  74. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  75.  96 else:
  76.  97 break
  77.  
  78. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 160000001 176313700) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 160000001 176313700) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/bc0bdd5f-dfe7-43b5-9a40-3d1888b0eb2f/tmp8Wb415/NA12878-1-sort-160000001_176313700-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d78e89f5-1a1d-44af-ab5d-47f76ada41a9/tmpYnQyqk/NA12878-1-sort-160000001_176313700-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ba32afa0-2972-4129-8d21-48a0979cb4d5/tmpab_qQl/NA12878-1-sort-160000001_176313700.bam /dev/stdin
  79. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  80. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  81. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  82. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  83. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  84. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  85. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  86. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  87. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  88. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  89. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  90. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  91. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  92. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  93. duplicating @RG line NA12878-1
  94. duplicating @PG line bwa
  95. duplicating @SQ line 1
  96. duplicating @SQ line 2
  97. duplicating @SQ line 3
  98. duplicating @SQ line 4
  99. duplicating @SQ line 5
  100. duplicating @SQ line 6
  101. duplicating @SQ line 7
  102. duplicating @SQ line 8
  103. duplicating @SQ line 9
  104. duplicating @SQ line 10
  105. duplicating @SQ line 11
  106. duplicating @SQ line 12
  107. duplicating @SQ line 13
  108. duplicating @SQ line 14
  109. duplicating @SQ line 15
  110. duplicating @SQ line 16
  111. duplicating @SQ line 17
  112. duplicating @SQ line 18
  113. duplicating @SQ line 19
  114. duplicating @SQ line 20
  115. duplicating @SQ line 21
  116. duplicating @SQ line 22
  117. duplicating @SQ line X
  118. duplicating @SQ line Y
  119. duplicating @SQ line MT
  120. duplicating @SQ line GL000207.1
  121. duplicating @SQ line GL000226.1
  122. duplicating @SQ line GL000229.1
  123. duplicating @SQ line GL000231.1
  124. duplicating @SQ line GL000210.1
  125. duplicating @SQ line GL000239.1
  126. duplicating @SQ line GL000235.1
  127. duplicating @SQ line GL000201.1
  128. duplicating @SQ line GL000247.1
  129. duplicating @SQ line GL000245.1
  130. duplicating @SQ line GL000197.1
  131. duplicating @SQ line GL000203.1
  132. duplicating @SQ line GL000246.1
  133. duplicating @SQ line GL000249.1
  134. duplicating @SQ line GL000196.1
  135. duplicating @SQ line GL000248.1
  136. duplicating @SQ line GL000244.1
  137. duplicating @SQ line GL000238.1
  138. duplicating @SQ line GL000202.1
  139. duplicating @SQ line GL000234.1
  140. duplicating @SQ line GL000232.1
  141. duplicating @SQ line GL000206.1
  142. duplicating @SQ line GL000240.1
  143. duplicating @SQ line GL000236.1
  144. duplicating @SQ line GL000241.1
  145. duplicating @SQ line GL000243.1
  146. duplicating @SQ line GL000242.1
  147. duplicating @SQ line GL000230.1
  148. duplicating @SQ line GL000237.1
  149. duplicating @SQ line GL000233.1
  150. duplicating @SQ line GL000204.1
  151. duplicating @SQ line GL000198.1
  152. duplicating @SQ line GL000208.1
  153. duplicating @SQ line GL000191.1
  154. duplicating @SQ line GL000227.1
  155. duplicating @SQ line GL000228.1
  156. duplicating @SQ line GL000214.1
  157. duplicating @SQ line GL000221.1
  158. duplicating @SQ line GL000209.1
  159. duplicating @SQ line GL000218.1
  160. duplicating @SQ line GL000220.1
  161. duplicating @SQ line GL000213.1
  162. duplicating @SQ line GL000211.1
  163. duplicating @SQ line GL000199.1
  164. duplicating @SQ line GL000217.1
  165. duplicating @SQ line GL000216.1
  166. duplicating @SQ line GL000215.1
  167. duplicating @SQ line GL000205.1
  168. duplicating @SQ line GL000219.1
  169. duplicating @SQ line GL000224.1
  170. duplicating @SQ line GL000223.1
  171. duplicating @SQ line GL000195.1
  172. duplicating @SQ line GL000212.1
  173. duplicating @SQ line GL000222.1
  174. duplicating @SQ line GL000200.1
  175. duplicating @SQ line GL000193.1
  176. duplicating @SQ line GL000194.1
  177. duplicating @SQ line GL000225.1
  178. duplicating @SQ line GL000192.1
  179. ' returned non-zero exit status 1
  180. cat: write error: Broken pipe
  181. 2016-07-28 00:20:25.145 [IPEngineApp] Exception in apply request:
  182. 
  183. CalledProcessErrorTraceback (most recent call last)
  184. <string> in <module>()
  185.  
  186. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  187.  71 
  188.  72 def __call__(self, *args, **kwargs):
  189. ---> 73 return self.f(*args, **kwargs)
  190.  74 
  191.  75 if not py3compat.PY3:
  192.  
  193. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  194.  179 args = ipython.unzip_args(args)
  195.  180 with _setup_logging(args) as config:
  196. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  197.  182 
  198.  183 @require(alignprep)
  199.  
  200. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  201.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  202.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  203. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  204.  113 data = _add_supplemental_bams(data)
  205.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  206.  
  207. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  208.  62 else:
  209.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  210. ---> 64 names, align_dir, data)
  211.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  212.  66 if not data.get("align_split"):
  213.  
  214. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  215.  115 config = data["config"]
  216.  116 align_fn = TOOLS[aligner].align_fn
  217. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  218.  118 # handle align functions that update the main data dictionary in place
  219.  119 if isinstance(out, dict):
  220.  
  221. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  222.  145 else:
  223.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  224. --> 147 names, rg_info, data)
  225.  148 data["work_bam"] = out_file
  226.  149 return data
  227.  
  228. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  229.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  230.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  231. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  232.  158 return out_file
  233.  159 
  234.  
  235. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  236.  19 try:
  237.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  238. ---> 21 _do_run(cmd, checks, log_stdout)
  239.  22 except:
  240.  23 diagnostics.end_cmd(cmd_id, False)
  241.  
  242. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  243.  93 s.communicate()
  244.  94 s.stdout.close()
  245. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  246.  96 else:
  247.  97 break
  248.  
  249. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 20000001 40000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 20000001 40000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/981265dc-2028-4a1b-9cd3-9edbeef33c78/tmp7kSXXE/NA12878-2-sort-20000001_40000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/59907c84-0d2d-40bd-bf8f-3f3d90706fd8/tmpJzwlnk/NA12878-2-sort-20000001_40000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d2beeaec-fd74-4579-b6a5-b7c5b90526f0/tmpG7iiH8/NA12878-2-sort-20000001_40000000.bam /dev/stdin
  250. samblaster: Version 0.1.22
  251. samblaster: Inputting from stdin
  252. samblaster: Outputting to stdout
  253. samblaster: Opening /dev/fd/62 for write.
  254. samblaster: Opening /dev/fd/63 for write.
  255. [W::bseq_read] the 2nd file has fewer sequences.
  256. [M::mem_pestat] skip orientation FF as there are not enough pairs
  257. [M::mem_pestat] skip orientation FR as there are not enough pairs
  258. [M::mem_pestat] skip orientation RF as there are not enough pairs
  259. [M::mem_pestat] skip orientation RR as there are not enough pairs
  260. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12361:170167", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  261.  
  262. [mem_sam_pe] samblaster: Loaded 84 header sequence entries.
  263. ' returned non-zero exit status 1
  264. cat: write error: Broken pipe
  265. 2016-07-28 00:20:46.480 [IPEngineApp] Exception in apply request:
  266. 
  267. CalledProcessErrorTraceback (most recent call last)
  268. <string> in <module>()
  269.  
  270. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  271.  71 
  272.  72 def __call__(self, *args, **kwargs):
  273. ---> 73 return self.f(*args, **kwargs)
  274.  74 
  275.  75 if not py3compat.PY3:
  276.  
  277. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  278.  179 args = ipython.unzip_args(args)
  279.  180 with _setup_logging(args) as config:
  280. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  281.  182 
  282.  183 @require(alignprep)
  283.  
  284. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  285.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  286.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  287. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  288.  113 data = _add_supplemental_bams(data)
  289.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  290.  
  291. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  292.  62 else:
  293.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  294. ---> 64 names, align_dir, data)
  295.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  296.  66 if not data.get("align_split"):
  297.  
  298. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  299.  115 config = data["config"]
  300.  116 align_fn = TOOLS[aligner].align_fn
  301. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  302.  118 # handle align functions that update the main data dictionary in place
  303.  119 if isinstance(out, dict):
  304.  
  305. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  306.  145 else:
  307.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  308. --> 147 names, rg_info, data)
  309.  148 data["work_bam"] = out_file
  310.  149 return data
  311.  
  312. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  313.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  314.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  315. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  316.  158 return out_file
  317.  159 
  318.  
  319. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  320.  19 try:
  321.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  322. ---> 21 _do_run(cmd, checks, log_stdout)
  323.  22 except:
  324.  23 diagnostics.end_cmd(cmd_id, False)
  325.  
  326. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  327.  93 s.communicate()
  328.  94 s.stdout.close()
  329. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  330.  96 else:
  331.  97 break
  332.  
  333. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 40000001 60000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 40000001 60000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b77edd90-f94c-4ba3-aa8e-11f65610e826/tmpRb3Fg2/NA12878-2-sort-40000001_60000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ee37cf82-ec3f-4c56-a3f1-ee0e3a7088e7/tmpmMqMrM/NA12878-2-sort-40000001_60000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/c836662c-9579-4938-bd8e-fbb2b4069414/tmpIHJrp5/NA12878-2-sort-40000001_60000000.bam /dev/stdin
  334. samblaster: Version 0.1.22
  335. samblaster: Inputting from stdin
  336. samblaster: Outputting to stdout
  337. samblaster: Opening /dev/fd/62 for write.
  338. samblaster: Opening /dev/fd/63 for write.
  339. [W::bseq_read] the 2nd file has fewer sequences.
  340. [M::mem_pestat] skip orientation FF as there are not enough pairs
  341. [M::mem_pestat] skip orientation FR as there are not enough pairs
  342. [M::mem_pestat] skip orientation RF as there are not enough pairs
  343. [M::mem_pestat] skip orientation RR as there are not enough pairs
  344. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16327:72117", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  345.  
  346. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16388:72120", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  347. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1204:16597:72069", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  348.  
  349.  
  350. samblaster: Loaded 84 header sequence entries.
  351. ' returned non-zero exit status 1
  352. cat: write error: Broken pipe
  353. 2016-07-28 00:21:37.050 [IPEngineApp] Exception in apply request:
  354. 
  355. CalledProcessErrorTraceback (most recent call last)
  356. <string> in <module>()
  357.  
  358. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  359.  71 
  360.  72 def __call__(self, *args, **kwargs):
  361. ---> 73 return self.f(*args, **kwargs)
  362.  74 
  363.  75 if not py3compat.PY3:
  364.  
  365. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  366.  179 args = ipython.unzip_args(args)
  367.  180 with _setup_logging(args) as config:
  368. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  369.  182 
  370.  183 @require(alignprep)
  371.  
  372. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  373.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  374.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  375. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  376.  113 data = _add_supplemental_bams(data)
  377.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  378.  
  379. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  380.  62 else:
  381.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  382. ---> 64 names, align_dir, data)
  383.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  384.  66 if not data.get("align_split"):
  385.  
  386. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  387.  115 config = data["config"]
  388.  116 align_fn = TOOLS[aligner].align_fn
  389. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  390.  118 # handle align functions that update the main data dictionary in place
  391.  119 if isinstance(out, dict):
  392.  
  393. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  394.  145 else:
  395.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  396. --> 147 names, rg_info, data)
  397.  148 data["work_bam"] = out_file
  398.  149 return data
  399.  
  400. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  401.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  402.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  403. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  404.  158 return out_file
  405.  159 
  406.  
  407. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  408.  19 try:
  409.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  410. ---> 21 _do_run(cmd, checks, log_stdout)
  411.  22 except:
  412.  23 diagnostics.end_cmd(cmd_id, False)
  413.  
  414. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  415.  93 s.communicate()
  416.  94 s.stdout.close()
  417. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  418.  96 else:
  419.  97 break
  420.  
  421. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 60000001 80000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 60000001 80000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/fb87f8e7-1a9f-4ab4-974c-fb20fb590d1d/tmpmHTlgw/NA12878-2-sort-60000001_80000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b4dbf326-b367-4c1f-8e3d-f15c9a7b6564/tmpsGM7Zh/NA12878-2-sort-60000001_80000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/eb8fc8d3-9265-45fc-a69b-8d42bfba0d64/tmpaPKyWK/NA12878-2-sort-60000001_80000000.bam /dev/stdin
  422. samblaster: Version 0.1.22
  423. samblaster: Inputting from stdin
  424. samblaster: Outputting to stdout
  425. samblaster: Opening /dev/fd/62 for write.
  426. samblaster: Opening /dev/fd/63 for write.
  427. [M::mem_pestat] skip orientation FF as there are not enough pairs
  428. [M::mem_pestat] skip orientation FR as there are not enough pairs
  429. [M::mem_pestat] skip orientation RF as there are not enough pairs
  430. [M::mem_pestat] skip orientation RR as there are not enough pairs
  431. [mem_sam_pe] [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20180:104496", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  432.  
  433. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20388:104287", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  434. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20287:104306", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  435.  
  436. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20615:104279", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  437. paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20315:104460", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  438.  
  439.  
  440. [mem_sam_pe]
  441. paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20356:104489", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  442.  
  443. paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20162:104468", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  444.  
  445. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20460:104376", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  446.  
  447. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1301:20279:104265", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  448.  
  449. samblaster: Loaded 84 header sequence entries.
  450. ' returned non-zero exit status 1
  451. cat: write error: Broken pipe
  452. 2016-07-28 00:21:58.797 [IPEngineApp] Exception in apply request:
  453. 
  454. CalledProcessErrorTraceback (most recent call last)
  455. <string> in <module>()
  456.  
  457. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  458.  71 
  459.  72 def __call__(self, *args, **kwargs):
  460. ---> 73 return self.f(*args, **kwargs)
  461.  74 
  462.  75 if not py3compat.PY3:
  463.  
  464. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  465.  179 args = ipython.unzip_args(args)
  466.  180 with _setup_logging(args) as config:
  467. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  468.  182 
  469.  183 @require(alignprep)
  470.  
  471. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  472.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  473.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  474. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  475.  113 data = _add_supplemental_bams(data)
  476.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  477.  
  478. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  479.  62 else:
  480.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  481. ---> 64 names, align_dir, data)
  482.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  483.  66 if not data.get("align_split"):
  484.  
  485. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  486.  115 config = data["config"]
  487.  116 align_fn = TOOLS[aligner].align_fn
  488. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  489.  118 # handle align functions that update the main data dictionary in place
  490.  119 if isinstance(out, dict):
  491.  
  492. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  493.  145 else:
  494.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  495. --> 147 names, rg_info, data)
  496.  148 data["work_bam"] = out_file
  497.  149 return data
  498.  
  499. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  500.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  501.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  502. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  503.  158 return out_file
  504.  159 
  505.  
  506. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  507.  19 try:
  508.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  509. ---> 21 _do_run(cmd, checks, log_stdout)
  510.  22 except:
  511.  23 diagnostics.end_cmd(cmd_id, False)
  512.  
  513. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  514.  93 s.communicate()
  515.  94 s.stdout.close()
  516. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  517.  96 else:
  518.  97 break
  519.  
  520. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 80000001 100000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 80000001 100000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/a8252421-66ad-4cba-8ce3-b58294ade9d2/tmp9sLFs9/NA12878-2-sort-80000001_100000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ee95b147-150d-4d5f-91e1-a2266236a8de/tmpSCdWLu/NA12878-2-sort-80000001_100000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b043c4a9-af9f-46e3-904a-4ea2b3e76795/tmpzWC3G6/NA12878-2-sort-80000001_100000000.bam /dev/stdin
  521. duplicating @SQ line GL000199.1
  522. duplicating @SQ line GL000217.1
  523. duplicating @SQ line GL000216.1
  524. duplicating @SQ line GL000215.1
  525. duplicating @SQ line GL000205.1
  526. duplicating @SQ line GL000219.1
  527. duplicating @SQ line GL000224.1
  528. duplicating @SQ line GL000223.1
  529. duplicating @SQ line GL000195.1
  530. duplicating @SQ line GL000212.1
  531. duplicating @SQ line GL000222.1
  532. duplicating @SQ line GL000200.1
  533. duplicating @SQ line GL000193.1
  534. duplicating @SQ line GL000194.1
  535. duplicating @SQ line GL000225.1
  536. duplicating @SQ line GL000192.1
  537. duplicating @SQ line 1
  538. duplicating @SQ line 2
  539. duplicating @SQ line 3
  540. duplicating @SQ line 4
  541. duplicating @SQ line 5
  542. duplicating @SQ line 6
  543. duplicating @SQ line 7
  544. duplicating @SQ line 8
  545. duplicating @SQ line 9
  546. duplicating @SQ line 10
  547. duplicating @SQ line 11
  548. duplicating @SQ line 12
  549. duplicating @SQ line 13
  550. duplicating @SQ line 14
  551. duplicating @SQ line 15
  552. duplicating @SQ line 16
  553. duplicating @SQ line 17
  554. duplicating @SQ line 18
  555. duplicating @SQ line 19
  556. duplicating @SQ line 20
  557. duplicating @SQ line 21
  558. duplicating @SQ line 22
  559. duplicating @SQ line X
  560. duplicating @SQ line Y
  561. duplicating @SQ line MT
  562. duplicating @SQ line GL000207.1
  563. duplicating @SQ line GL000226.1
  564. duplicating @SQ line GL000229.1
  565. duplicating @SQ line GL000231.1
  566. duplicating @SQ line GL000210.1
  567. duplicating @SQ line GL000239.1
  568. duplicating @SQ line GL000235.1
  569. duplicating @SQ line GL000201.1
  570. duplicating @SQ line GL000247.1
  571. duplicating @SQ line GL000245.1
  572. duplicating @SQ line GL000197.1
  573. duplicating @SQ line GL000203.1
  574. duplicating @SQ line GL000246.1
  575. duplicating @SQ line GL000249.1
  576. duplicating @SQ line GL000196.1
  577. duplicating @SQ line GL000248.1
  578. duplicating @SQ line GL000244.1
  579. duplicating @SQ line GL000238.1
  580. duplicating @SQ line GL000202.1
  581. duplicating @SQ line GL000234.1
  582. duplicating @SQ line GL000232.1
  583. duplicating @SQ line GL000206.1
  584. duplicating @SQ line GL000240.1
  585. duplicating @SQ line GL000236.1
  586. duplicating @SQ line GL000241.1
  587. duplicating @SQ line GL000243.1
  588. duplicating @SQ line GL000242.1
  589. duplicating @SQ line GL000230.1
  590. duplicating @SQ line GL000237.1
  591. duplicating @SQ line GL000233.1
  592. duplicating @SQ line GL000204.1
  593. duplicating @SQ line GL000198.1
  594. duplicating @SQ line GL000208.1
  595. duplicating @SQ line GL000191.1
  596. duplicating @SQ line GL000227.1
  597. duplicating @SQ line GL000228.1
  598. duplicating @SQ line GL000214.1
  599. duplicating @SQ line GL000221.1
  600. duplicating @SQ line GL000209.1
  601. duplicating @SQ line GL000218.1
  602. duplicating @SQ line GL000220.1
  603. duplicating @SQ line GL000213.1
  604. duplicating @SQ line GL000211.1
  605. duplicating @SQ line GL000199.1
  606. duplicating @SQ line GL000217.1
  607. duplicating @SQ line GL000216.1
  608. duplicating @SQ line GL000215.1
  609. duplicating @SQ line GL000205.1
  610. duplicating @SQ line GL000219.1
  611. duplicating @SQ line GL000224.1
  612. duplicating @SQ line GL000223.1
  613. duplicating @SQ line GL000195.1
  614. duplicating @SQ line GL000212.1
  615. duplicating @SQ line GL000222.1
  616. duplicating @SQ line GL000200.1
  617. duplicating @SQ line GL000193.1
  618. duplicating @SQ line GL000194.1
  619. duplicating @SQ line GL000225.1
  620. duplicating @SQ line GL000192.1
  621. ' returned non-zero exit status 1
  622. cat: write error: Broken pipe
  623. 2016-07-28 00:22:20.649 [IPEngineApp] Exception in apply request:
  624. 
  625. CalledProcessErrorTraceback (most recent call last)
  626. <string> in <module>()
  627.  
  628. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  629.  71 
  630.  72 def __call__(self, *args, **kwargs):
  631. ---> 73 return self.f(*args, **kwargs)
  632.  74 
  633.  75 if not py3compat.PY3:
  634.  
  635. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  636.  179 args = ipython.unzip_args(args)
  637.  180 with _setup_logging(args) as config:
  638. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  639.  182 
  640.  183 @require(alignprep)
  641.  
  642. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  643.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  644.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  645. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  646.  113 data = _add_supplemental_bams(data)
  647.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  648.  
  649. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  650.  62 else:
  651.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  652. ---> 64 names, align_dir, data)
  653.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  654.  66 if not data.get("align_split"):
  655.  
  656. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  657.  115 config = data["config"]
  658.  116 align_fn = TOOLS[aligner].align_fn
  659. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  660.  118 # handle align functions that update the main data dictionary in place
  661.  119 if isinstance(out, dict):
  662.  
  663. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  664.  145 else:
  665.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  666. --> 147 names, rg_info, data)
  667.  148 data["work_bam"] = out_file
  668.  149 return data
  669.  
  670. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  671.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  672.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  673. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  674.  158 return out_file
  675.  159 
  676.  
  677. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  678.  19 try:
  679.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  680. ---> 21 _do_run(cmd, checks, log_stdout)
  681.  22 except:
  682.  23 diagnostics.end_cmd(cmd_id, False)
  683.  
  684. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  685.  93 s.communicate()
  686.  94 s.stdout.close()
  687. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  688.  96 else:
  689.  97 break
  690.  
  691. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 100000001 120000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 100000001 120000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/93cc0d04-3311-4891-ae89-e6043a917d59/tmppQu0Kn/NA12878-2-sort-100000001_120000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/93a9a601-13d6-44ec-8e40-a614b47ae28b/tmpf9ROae/NA12878-2-sort-100000001_120000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/019bc707-7f20-4b2c-bc72-5c27c8de97a4/tmpbhVMW7/NA12878-2-sort-100000001_120000000.bam /dev/stdin
  692. duplicating @SQ line GL000199.1
  693. duplicating @SQ line GL000217.1
  694. duplicating @SQ line GL000216.1
  695. duplicating @SQ line GL000215.1
  696. duplicating @SQ line GL000205.1
  697. duplicating @SQ line GL000219.1
  698. duplicating @SQ line GL000224.1
  699. duplicating @SQ line GL000223.1
  700. duplicating @SQ line GL000195.1
  701. duplicating @SQ line GL000212.1
  702. duplicating @SQ line GL000222.1
  703. duplicating @SQ line GL000200.1
  704. duplicating @SQ line GL000193.1
  705. duplicating @SQ line GL000194.1
  706. duplicating @SQ line GL000225.1
  707. duplicating @SQ line GL000192.1
  708. duplicating @SQ line 1
  709. duplicating @SQ line 2
  710. duplicating @SQ line 3
  711. duplicating @SQ line 4
  712. duplicating @SQ line 5
  713. duplicating @SQ line 6
  714. duplicating @SQ line 7
  715. duplicating @SQ line 8
  716. duplicating @SQ line 9
  717. duplicating @SQ line 10
  718. duplicating @SQ line 11
  719. duplicating @SQ line 12
  720. duplicating @SQ line 13
  721. duplicating @SQ line 14
  722. duplicating @SQ line 15
  723. duplicating @SQ line 16
  724. duplicating @SQ line 17
  725. duplicating @SQ line 18
  726. duplicating @SQ line 19
  727. duplicating @SQ line 20
  728. duplicating @SQ line 21
  729. duplicating @SQ line 22
  730. duplicating @SQ line X
  731. duplicating @SQ line Y
  732. duplicating @SQ line MT
  733. duplicating @SQ line GL000207.1
  734. duplicating @SQ line GL000226.1
  735. duplicating @SQ line GL000229.1
  736. duplicating @SQ line GL000231.1
  737. duplicating @SQ line GL000210.1
  738. duplicating @SQ line GL000239.1
  739. duplicating @SQ line GL000235.1
  740. duplicating @SQ line GL000201.1
  741. duplicating @SQ line GL000247.1
  742. duplicating @SQ line GL000245.1
  743. duplicating @SQ line GL000197.1
  744. duplicating @SQ line GL000203.1
  745. duplicating @SQ line GL000246.1
  746. duplicating @SQ line GL000249.1
  747. duplicating @SQ line GL000196.1
  748. duplicating @SQ line GL000248.1
  749. duplicating @SQ line GL000244.1
  750. duplicating @SQ line GL000238.1
  751. duplicating @SQ line GL000202.1
  752. duplicating @SQ line GL000234.1
  753. duplicating @SQ line GL000232.1
  754. duplicating @SQ line GL000206.1
  755. duplicating @SQ line GL000240.1
  756. duplicating @SQ line GL000236.1
  757. duplicating @SQ line GL000241.1
  758. duplicating @SQ line GL000243.1
  759. duplicating @SQ line GL000242.1
  760. duplicating @SQ line GL000230.1
  761. duplicating @SQ line GL000237.1
  762. duplicating @SQ line GL000233.1
  763. duplicating @SQ line GL000204.1
  764. duplicating @SQ line GL000198.1
  765. duplicating @SQ line GL000208.1
  766. duplicating @SQ line GL000191.1
  767. duplicating @SQ line GL000227.1
  768. duplicating @SQ line GL000228.1
  769. duplicating @SQ line GL000214.1
  770. duplicating @SQ line GL000221.1
  771. duplicating @SQ line GL000209.1
  772. duplicating @SQ line GL000218.1
  773. duplicating @SQ line GL000220.1
  774. duplicating @SQ line GL000213.1
  775. duplicating @SQ line GL000211.1
  776. duplicating @SQ line GL000199.1
  777. duplicating @SQ line GL000217.1
  778. duplicating @SQ line GL000216.1
  779. duplicating @SQ line GL000215.1
  780. duplicating @SQ line GL000205.1
  781. duplicating @SQ line GL000219.1
  782. duplicating @SQ line GL000224.1
  783. duplicating @SQ line GL000223.1
  784. duplicating @SQ line GL000195.1
  785. duplicating @SQ line GL000212.1
  786. duplicating @SQ line GL000222.1
  787. duplicating @SQ line GL000200.1
  788. duplicating @SQ line GL000193.1
  789. duplicating @SQ line GL000194.1
  790. duplicating @SQ line GL000225.1
  791. duplicating @SQ line GL000192.1
  792. ' returned non-zero exit status 1
  793. cat: write error: Broken pipe
  794. 2016-07-28 00:23:12.207 [IPEngineApp] Exception in apply request:
  795. 
  796. CalledProcessErrorTraceback (most recent call last)
  797. <string> in <module>()
  798.  
  799. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  800.  71 
  801.  72 def __call__(self, *args, **kwargs):
  802. ---> 73 return self.f(*args, **kwargs)
  803.  74 
  804.  75 if not py3compat.PY3:
  805.  
  806. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  807.  179 args = ipython.unzip_args(args)
  808.  180 with _setup_logging(args) as config:
  809. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  810.  182 
  811.  183 @require(alignprep)
  812.  
  813. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  814.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  815.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  816. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  817.  113 data = _add_supplemental_bams(data)
  818.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  819.  
  820. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  821.  62 else:
  822.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  823. ---> 64 names, align_dir, data)
  824.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  825.  66 if not data.get("align_split"):
  826.  
  827. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  828.  115 config = data["config"]
  829.  116 align_fn = TOOLS[aligner].align_fn
  830. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  831.  118 # handle align functions that update the main data dictionary in place
  832.  119 if isinstance(out, dict):
  833.  
  834. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  835.  145 else:
  836.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  837. --> 147 names, rg_info, data)
  838.  148 data["work_bam"] = out_file
  839.  149 return data
  840.  
  841. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  842.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  843.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  844. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  845.  158 return out_file
  846.  159 
  847.  
  848. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  849.  19 try:
  850.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  851. ---> 21 _do_run(cmd, checks, log_stdout)
  852.  22 except:
  853.  23 diagnostics.end_cmd(cmd_id, False)
  854.  
  855. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  856.  93 s.communicate()
  857.  94 s.stdout.close()
  858. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  859.  96 else:
  860.  97 break
  861.  
  862. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 120000001 140000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 120000001 140000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/e440d58e-f06e-48e9-9ed0-28dadf43ce0a/tmpaAAYTV/NA12878-2-sort-120000001_140000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/d792855b-9795-419d-be5e-8da29029b8e7/tmpjVaAhU/NA12878-2-sort-120000001_140000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/6acef7b1-e644-4023-9b9b-998c9b2de3dc/tmpTRl0G9/NA12878-2-sort-120000001_140000000.bam /dev/stdin
  863. samblaster: Version 0.1.22
  864. samblaster: Inputting from stdin
  865. samblaster: Outputting to stdout
  866. samblaster: Opening /dev/fd/62 for write.
  867. samblaster: Opening /dev/fd/63 for write.
  868. [M::mem_pestat] skip orientation FF as there are not enough pairs
  869. [M::mem_pestat] skip orientation FR as there are not enough pairs
  870. [M::mem_pestat] skip orientation RF as there are not enough pairs
  871. [M::mem_pestat] skip orientation RR as there are not enough pairs
  872. [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20705:113542", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  873. paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20717:113626", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  874.  
  875.  
  876. [mem_sam_pe] samblaster: Loaded 84 header sequence entries.
  877. ' returned non-zero exit status 1
  878. cat: write error: Broken pipe
  879. 2016-07-28 00:24:04.510 [IPEngineApp] Exception in apply request:
  880. 
  881. CalledProcessErrorTraceback (most recent call last)
  882. <string> in <module>()
  883.  
  884. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  885.  71 
  886.  72 def __call__(self, *args, **kwargs):
  887. ---> 73 return self.f(*args, **kwargs)
  888.  74 
  889.  75 if not py3compat.PY3:
  890.  
  891. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  892.  179 args = ipython.unzip_args(args)
  893.  180 with _setup_logging(args) as config:
  894. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  895.  182 
  896.  183 @require(alignprep)
  897.  
  898. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  899.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  900.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  901. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  902.  113 data = _add_supplemental_bams(data)
  903.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  904.  
  905. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  906.  62 else:
  907.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  908. ---> 64 names, align_dir, data)
  909.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  910.  66 if not data.get("align_split"):
  911.  
  912. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  913.  115 config = data["config"]
  914.  116 align_fn = TOOLS[aligner].align_fn
  915. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  916.  118 # handle align functions that update the main data dictionary in place
  917.  119 if isinstance(out, dict):
  918.  
  919. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  920.  145 else:
  921.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  922. --> 147 names, rg_info, data)
  923.  148 data["work_bam"] = out_file
  924.  149 return data
  925.  
  926. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  927.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  928.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  929. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  930.  158 return out_file
  931.  159 
  932.  
  933. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  934.  19 try:
  935.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  936. ---> 21 _do_run(cmd, checks, log_stdout)
  937.  22 except:
  938.  23 diagnostics.end_cmd(cmd_id, False)
  939.  
  940. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  941.  93 s.communicate()
  942.  94 s.stdout.close()
  943. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  944.  96 else:
  945.  97 break
  946.  
  947. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 140000001 160000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 140000001 160000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/be00c357-c469-4c6f-ad58-ef2819779dbc/tmpmDlRz4/NA12878-2-sort-140000001_160000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/434305af-775e-4e61-8f32-a63845b043dc/tmpLHG6EA/NA12878-2-sort-140000001_160000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8e239e80-9d03-4f87-a379-154e8db376da/tmpCbixFJ/NA12878-2-sort-140000001_160000000.bam /dev/stdin
  948. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  949. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  950. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  951. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  952. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  953. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  954. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  955. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  956. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  957. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  958. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  959. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  960. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  961. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  962. duplicating @RG line NA12878-2
  963. duplicating @PG line bwa
  964. duplicating @SQ line 1
  965. duplicating @SQ line 2
  966. duplicating @SQ line 3
  967. duplicating @SQ line 4
  968. duplicating @SQ line 5
  969. duplicating @SQ line 6
  970. duplicating @SQ line 7
  971. duplicating @SQ line 8
  972. duplicating @SQ line 9
  973. duplicating @SQ line 10
  974. duplicating @SQ line 11
  975. duplicating @SQ line 12
  976. duplicating @SQ line 13
  977. duplicating @SQ line 14
  978. duplicating @SQ line 15
  979. duplicating @SQ line 16
  980. duplicating @SQ line 17
  981. duplicating @SQ line 18
  982. duplicating @SQ line 19
  983. duplicating @SQ line 20
  984. duplicating @SQ line 21
  985. duplicating @SQ line 22
  986. duplicating @SQ line X
  987. duplicating @SQ line Y
  988. duplicating @SQ line MT
  989. duplicating @SQ line GL000207.1
  990. duplicating @SQ line GL000226.1
  991. duplicating @SQ line GL000229.1
  992. duplicating @SQ line GL000231.1
  993. duplicating @SQ line GL000210.1
  994. duplicating @SQ line GL000239.1
  995. duplicating @SQ line GL000235.1
  996. duplicating @SQ line GL000201.1
  997. duplicating @SQ line GL000247.1
  998. duplicating @SQ line GL000245.1
  999. duplicating @SQ line GL000197.1
  1000. duplicating @SQ line GL000203.1
  1001. duplicating @SQ line GL000246.1
  1002. duplicating @SQ line GL000249.1
  1003. duplicating @SQ line GL000196.1
  1004. duplicating @SQ line GL000248.1
  1005. duplicating @SQ line GL000244.1
  1006. duplicating @SQ line GL000238.1
  1007. duplicating @SQ line GL000202.1
  1008. duplicating @SQ line GL000234.1
  1009. duplicating @SQ line GL000232.1
  1010. duplicating @SQ line GL000206.1
  1011. duplicating @SQ line GL000240.1
  1012. duplicating @SQ line GL000236.1
  1013. duplicating @SQ line GL000241.1
  1014. duplicating @SQ line GL000243.1
  1015. duplicating @SQ line GL000242.1
  1016. duplicating @SQ line GL000230.1
  1017. duplicating @SQ line GL000237.1
  1018. duplicating @SQ line GL000233.1
  1019. duplicating @SQ line GL000204.1
  1020. duplicating @SQ line GL000198.1
  1021. duplicating @SQ line GL000208.1
  1022. duplicating @SQ line GL000191.1
  1023. duplicating @SQ line GL000227.1
  1024. duplicating @SQ line GL000228.1
  1025. duplicating @SQ line GL000214.1
  1026. duplicating @SQ line GL000221.1
  1027. duplicating @SQ line GL000209.1
  1028. duplicating @SQ line GL000218.1
  1029. duplicating @SQ line GL000220.1
  1030. duplicating @SQ line GL000213.1
  1031. duplicating @SQ line GL000211.1
  1032. duplicating @SQ line GL000199.1
  1033. duplicating @SQ line GL000217.1
  1034. duplicating @SQ line GL000216.1
  1035. duplicating @SQ line GL000215.1
  1036. duplicating @SQ line GL000205.1
  1037. duplicating @SQ line GL000219.1
  1038. duplicating @SQ line GL000224.1
  1039. duplicating @SQ line GL000223.1
  1040. duplicating @SQ line GL000195.1
  1041. duplicating @SQ line GL000212.1
  1042. duplicating @SQ line GL000222.1
  1043. duplicating @SQ line GL000200.1
  1044. duplicating @SQ line GL000193.1
  1045. duplicating @SQ line GL000194.1
  1046. duplicating @SQ line GL000225.1
  1047. duplicating @SQ line GL000192.1
  1048. ' returned non-zero exit status 1
  1049. cat: write error: Broken pipe
  1050. 2016-07-28 00:24:24.822 [IPEngineApp] Exception in apply request:
  1051. 
  1052. CalledProcessErrorTraceback (most recent call last)
  1053. <string> in <module>()
  1054.  
  1055. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1056.  71 
  1057.  72 def __call__(self, *args, **kwargs):
  1058. ---> 73 return self.f(*args, **kwargs)
  1059.  74 
  1060.  75 if not py3compat.PY3:
  1061.  
  1062. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1063.  179 args = ipython.unzip_args(args)
  1064.  180 with _setup_logging(args) as config:
  1065. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1066.  182 
  1067.  183 @require(alignprep)
  1068.  
  1069. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1070.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1071.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1072. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1073.  113 data = _add_supplemental_bams(data)
  1074.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1075.  
  1076. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1077.  62 else:
  1078.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1079. ---> 64 names, align_dir, data)
  1080.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1081.  66 if not data.get("align_split"):
  1082.  
  1083. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1084.  115 config = data["config"]
  1085.  116 align_fn = TOOLS[aligner].align_fn
  1086. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1087.  118 # handle align functions that update the main data dictionary in place
  1088.  119 if isinstance(out, dict):
  1089.  
  1090. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1091.  145 else:
  1092.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1093. --> 147 names, rg_info, data)
  1094.  148 data["work_bam"] = out_file
  1095.  149 return data
  1096.  
  1097. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1098.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1099.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1100. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1101.  158 return out_file
  1102.  159 
  1103.  
  1104. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1105.  19 try:
  1106.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1107. ---> 21 _do_run(cmd, checks, log_stdout)
  1108.  22 except:
  1109.  23 diagnostics.end_cmd(cmd_id, False)
  1110.  
  1111. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1112.  93 s.communicate()
  1113.  94 s.stdout.close()
  1114. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1115.  96 else:
  1116.  97 break
  1117.  
  1118. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 20000001 40000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 20000001 40000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0b2a4e51-fdd7-486c-89f9-5e2106fb6b58/tmpeaxP4G/NA12878-1-sort-20000001_40000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0580ef0c-ae5e-4af2-a11e-6598a9b340c6/tmp_nXdx7/NA12878-1-sort-20000001_40000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/af4269bd-f10e-4720-a1a0-d198e7dea2bb/tmpToEq1V/NA12878-1-sort-20000001_40000000.bam /dev/stdin
  1119. samblaster: Version 0.1.22
  1120. samblaster: Inputting from stdin
  1121. samblaster: Outputting to stdout
  1122. samblaster: Opening /dev/fd/62 for write.
  1123. samblaster: Opening /dev/fd/63 for write.
  1124. [W::bseq_read] the 2nd file has fewer sequences.
  1125. [M::mem_pestat] skip orientation FF as there are not enough pairs
  1126. [M::mem_pestat] skip orientation FR as there are not enough pairs
  1127. [M::mem_pestat] skip orientation RF as there are not enough pairs
  1128. [M::mem_pestat] skip orientation RR as there are not enough pairs
  1129. [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12312:170243", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  1130.  
  1131. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:1106:12395:170197", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  1132. [mem_sam_pe]
  1133. samblaster: Loaded 84 header sequence entries.
  1134. ' returned non-zero exit status 1
  1135. cat: write error: Broken pipe
  1136. 2016-07-28 00:25:16.471 [IPEngineApp] Exception in apply request:
  1137. 
  1138. CalledProcessErrorTraceback (most recent call last)
  1139. <string> in <module>()
  1140.  
  1141. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1142.  71 
  1143.  72 def __call__(self, *args, **kwargs):
  1144. ---> 73 return self.f(*args, **kwargs)
  1145.  74 
  1146.  75 if not py3compat.PY3:
  1147.  
  1148. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1149.  179 args = ipython.unzip_args(args)
  1150.  180 with _setup_logging(args) as config:
  1151. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1152.  182 
  1153.  183 @require(alignprep)
  1154.  
  1155. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1156.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1157.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1158. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1159.  113 data = _add_supplemental_bams(data)
  1160.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1161.  
  1162. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1163.  62 else:
  1164.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1165. ---> 64 names, align_dir, data)
  1166.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1167.  66 if not data.get("align_split"):
  1168.  
  1169. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1170.  115 config = data["config"]
  1171.  116 align_fn = TOOLS[aligner].align_fn
  1172. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1173.  118 # handle align functions that update the main data dictionary in place
  1174.  119 if isinstance(out, dict):
  1175.  
  1176. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1177.  145 else:
  1178.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1179. --> 147 names, rg_info, data)
  1180.  148 data["work_bam"] = out_file
  1181.  149 return data
  1182.  
  1183. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1184.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1185.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1186. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1187.  158 return out_file
  1188.  159 
  1189.  
  1190. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1191.  19 try:
  1192.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1193. ---> 21 _do_run(cmd, checks, log_stdout)
  1194.  22 except:
  1195.  23 diagnostics.end_cmd(cmd_id, False)
  1196.  
  1197. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1198.  93 s.communicate()
  1199.  94 s.stdout.close()
  1200. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1201.  96 else:
  1202.  97 break
  1203.  
  1204. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 140000001 160000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 140000001 160000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/11059b50-cc75-445d-af19-cab36c0ac036/tmp4_21V4/NA12878-1-sort-140000001_160000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/70a00351-292c-4622-96c5-0d39f7564844/tmpxIdHOp/NA12878-1-sort-140000001_160000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/50889a34-56fb-4439-9ef7-4c2e669abbe9/tmpbPyql6/NA12878-1-sort-140000001_160000000.bam /dev/stdin
  1205. duplicating @SQ line GL000199.1
  1206. duplicating @SQ line GL000217.1
  1207. duplicating @SQ line GL000216.1
  1208. duplicating @SQ line GL000215.1
  1209. duplicating @SQ line GL000205.1
  1210. duplicating @SQ line GL000219.1
  1211. duplicating @SQ line GL000224.1
  1212. duplicating @SQ line GL000223.1
  1213. duplicating @SQ line GL000195.1
  1214. duplicating @SQ line GL000212.1
  1215. duplicating @SQ line GL000222.1
  1216. duplicating @SQ line GL000200.1
  1217. duplicating @SQ line GL000193.1
  1218. duplicating @SQ line GL000194.1
  1219. duplicating @SQ line GL000225.1
  1220. duplicating @SQ line GL000192.1
  1221. duplicating @SQ line 1
  1222. duplicating @SQ line 2
  1223. duplicating @SQ line 3
  1224. duplicating @SQ line 4
  1225. duplicating @SQ line 5
  1226. duplicating @SQ line 6
  1227. duplicating @SQ line 7
  1228. duplicating @SQ line 8
  1229. duplicating @SQ line 9
  1230. duplicating @SQ line 10
  1231. duplicating @SQ line 11
  1232. duplicating @SQ line 12
  1233. duplicating @SQ line 13
  1234. duplicating @SQ line 14
  1235. duplicating @SQ line 15
  1236. duplicating @SQ line 16
  1237. duplicating @SQ line 17
  1238. duplicating @SQ line 18
  1239. duplicating @SQ line 19
  1240. duplicating @SQ line 20
  1241. duplicating @SQ line 21
  1242. duplicating @SQ line 22
  1243. duplicating @SQ line X
  1244. duplicating @SQ line Y
  1245. duplicating @SQ line MT
  1246. duplicating @SQ line GL000207.1
  1247. duplicating @SQ line GL000226.1
  1248. duplicating @SQ line GL000229.1
  1249. duplicating @SQ line GL000231.1
  1250. duplicating @SQ line GL000210.1
  1251. duplicating @SQ line GL000239.1
  1252. duplicating @SQ line GL000235.1
  1253. duplicating @SQ line GL000201.1
  1254. duplicating @SQ line GL000247.1
  1255. duplicating @SQ line GL000245.1
  1256. duplicating @SQ line GL000197.1
  1257. duplicating @SQ line GL000203.1
  1258. duplicating @SQ line GL000246.1
  1259. duplicating @SQ line GL000249.1
  1260. duplicating @SQ line GL000196.1
  1261. duplicating @SQ line GL000248.1
  1262. duplicating @SQ line GL000244.1
  1263. duplicating @SQ line GL000238.1
  1264. duplicating @SQ line GL000202.1
  1265. duplicating @SQ line GL000234.1
  1266. duplicating @SQ line GL000232.1
  1267. duplicating @SQ line GL000206.1
  1268. duplicating @SQ line GL000240.1
  1269. duplicating @SQ line GL000236.1
  1270. duplicating @SQ line GL000241.1
  1271. duplicating @SQ line GL000243.1
  1272. duplicating @SQ line GL000242.1
  1273. duplicating @SQ line GL000230.1
  1274. duplicating @SQ line GL000237.1
  1275. duplicating @SQ line GL000233.1
  1276. duplicating @SQ line GL000204.1
  1277. duplicating @SQ line GL000198.1
  1278. duplicating @SQ line GL000208.1
  1279. duplicating @SQ line GL000191.1
  1280. duplicating @SQ line GL000227.1
  1281. duplicating @SQ line GL000228.1
  1282. duplicating @SQ line GL000214.1
  1283. duplicating @SQ line GL000221.1
  1284. duplicating @SQ line GL000209.1
  1285. duplicating @SQ line GL000218.1
  1286. duplicating @SQ line GL000220.1
  1287. duplicating @SQ line GL000213.1
  1288. duplicating @SQ line GL000211.1
  1289. duplicating @SQ line GL000199.1
  1290. duplicating @SQ line GL000217.1
  1291. duplicating @SQ line GL000216.1
  1292. duplicating @SQ line GL000215.1
  1293. duplicating @SQ line GL000205.1
  1294. duplicating @SQ line GL000219.1
  1295. duplicating @SQ line GL000224.1
  1296. duplicating @SQ line GL000223.1
  1297. duplicating @SQ line GL000195.1
  1298. duplicating @SQ line GL000212.1
  1299. duplicating @SQ line GL000222.1
  1300. duplicating @SQ line GL000200.1
  1301. duplicating @SQ line GL000193.1
  1302. duplicating @SQ line GL000194.1
  1303. duplicating @SQ line GL000225.1
  1304. duplicating @SQ line GL000192.1
  1305. ' returned non-zero exit status 1
  1306. cat: write error: Broken pipe
  1307. 2016-07-28 00:25:39.162 [IPEngineApp] Exception in apply request:
  1308. 
  1309. CalledProcessErrorTraceback (most recent call last)
  1310. <string> in <module>()
  1311.  
  1312. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1313.  71 
  1314.  72 def __call__(self, *args, **kwargs):
  1315. ---> 73 return self.f(*args, **kwargs)
  1316.  74 
  1317.  75 if not py3compat.PY3:
  1318.  
  1319. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1320.  179 args = ipython.unzip_args(args)
  1321.  180 with _setup_logging(args) as config:
  1322. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1323.  182 
  1324.  183 @require(alignprep)
  1325.  
  1326. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1327.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1328.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1329. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1330.  113 data = _add_supplemental_bams(data)
  1331.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1332.  
  1333. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1334.  62 else:
  1335.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1336. ---> 64 names, align_dir, data)
  1337.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1338.  66 if not data.get("align_split"):
  1339.  
  1340. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1341.  115 config = data["config"]
  1342.  116 align_fn = TOOLS[aligner].align_fn
  1343. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1344.  118 # handle align functions that update the main data dictionary in place
  1345.  119 if isinstance(out, dict):
  1346.  
  1347. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1348.  145 else:
  1349.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1350. --> 147 names, rg_info, data)
  1351.  148 data["work_bam"] = out_file
  1352.  149 return data
  1353.  
  1354. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1355.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1356.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1357. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1358.  158 return out_file
  1359.  159 
  1360.  
  1361. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1362.  19 try:
  1363.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1364. ---> 21 _do_run(cmd, checks, log_stdout)
  1365.  22 except:
  1366.  23 diagnostics.end_cmd(cmd_id, False)
  1367.  
  1368. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1369.  93 s.communicate()
  1370.  94 s.stdout.close()
  1371. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1372.  96 else:
  1373.  97 break
  1374.  
  1375. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 40000001 60000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 40000001 60000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0c640066-4500-4885-9b67-054cbc2a43f1/tmpab_NFG/NA12878-1-sort-40000001_60000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/b9e37910-f953-4684-b5cc-fc55b99b5b6f/tmpQouZrN/NA12878-1-sort-40000001_60000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/795eca19-e8ea-4975-b3f1-dfa313fa510d/tmp4q7JE4/NA12878-1-sort-40000001_60000000.bam /dev/stdin
  1376. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  1377. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  1378. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  1379. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  1380. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  1381. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  1382. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  1383. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  1384. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  1385. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  1386. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  1387. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  1388. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  1389. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  1390. duplicating @RG line NA12878-1
  1391. duplicating @PG line bwa
  1392. duplicating @SQ line 1
  1393. duplicating @SQ line 2
  1394. duplicating @SQ line 3
  1395. duplicating @SQ line 4
  1396. duplicating @SQ line 5
  1397. duplicating @SQ line 6
  1398. duplicating @SQ line 7
  1399. duplicating @SQ line 8
  1400. duplicating @SQ line 9
  1401. duplicating @SQ line 10
  1402. duplicating @SQ line 11
  1403. duplicating @SQ line 12
  1404. duplicating @SQ line 13
  1405. duplicating @SQ line 14
  1406. duplicating @SQ line 15
  1407. duplicating @SQ line 16
  1408. duplicating @SQ line 17
  1409. duplicating @SQ line 18
  1410. duplicating @SQ line 19
  1411. duplicating @SQ line 20
  1412. duplicating @SQ line 21
  1413. duplicating @SQ line 22
  1414. duplicating @SQ line X
  1415. duplicating @SQ line Y
  1416. duplicating @SQ line MT
  1417. duplicating @SQ line GL000207.1
  1418. duplicating @SQ line GL000226.1
  1419. duplicating @SQ line GL000229.1
  1420. duplicating @SQ line GL000231.1
  1421. duplicating @SQ line GL000210.1
  1422. duplicating @SQ line GL000239.1
  1423. duplicating @SQ line GL000235.1
  1424. duplicating @SQ line GL000201.1
  1425. duplicating @SQ line GL000247.1
  1426. duplicating @SQ line GL000245.1
  1427. duplicating @SQ line GL000197.1
  1428. duplicating @SQ line GL000203.1
  1429. duplicating @SQ line GL000246.1
  1430. duplicating @SQ line GL000249.1
  1431. duplicating @SQ line GL000196.1
  1432. duplicating @SQ line GL000248.1
  1433. duplicating @SQ line GL000244.1
  1434. duplicating @SQ line GL000238.1
  1435. duplicating @SQ line GL000202.1
  1436. duplicating @SQ line GL000234.1
  1437. duplicating @SQ line GL000232.1
  1438. duplicating @SQ line GL000206.1
  1439. duplicating @SQ line GL000240.1
  1440. duplicating @SQ line GL000236.1
  1441. duplicating @SQ line GL000241.1
  1442. duplicating @SQ line GL000243.1
  1443. duplicating @SQ line GL000242.1
  1444. duplicating @SQ line GL000230.1
  1445. duplicating @SQ line GL000237.1
  1446. duplicating @SQ line GL000233.1
  1447. duplicating @SQ line GL000204.1
  1448. duplicating @SQ line GL000198.1
  1449. duplicating @SQ line GL000208.1
  1450. duplicating @SQ line GL000191.1
  1451. duplicating @SQ line GL000227.1
  1452. duplicating @SQ line GL000228.1
  1453. duplicating @SQ line GL000214.1
  1454. duplicating @SQ line GL000221.1
  1455. duplicating @SQ line GL000209.1
  1456. duplicating @SQ line GL000218.1
  1457. duplicating @SQ line GL000220.1
  1458. duplicating @SQ line GL000213.1
  1459. duplicating @SQ line GL000211.1
  1460. duplicating @SQ line GL000199.1
  1461. duplicating @SQ line GL000217.1
  1462. duplicating @SQ line GL000216.1
  1463. duplicating @SQ line GL000215.1
  1464. duplicating @SQ line GL000205.1
  1465. duplicating @SQ line GL000219.1
  1466. duplicating @SQ line GL000224.1
  1467. duplicating @SQ line GL000223.1
  1468. duplicating @SQ line GL000195.1
  1469. duplicating @SQ line GL000212.1
  1470. duplicating @SQ line GL000222.1
  1471. duplicating @SQ line GL000200.1
  1472. duplicating @SQ line GL000193.1
  1473. duplicating @SQ line GL000194.1
  1474. duplicating @SQ line GL000225.1
  1475. duplicating @SQ line GL000192.1
  1476. ' returned non-zero exit status 1
  1477. cat: write error: Broken pipe
  1478. 2016-07-28 00:26:30.179 [IPEngineApp] Exception in apply request:
  1479. 
  1480. CalledProcessErrorTraceback (most recent call last)
  1481. <string> in <module>()
  1482.  
  1483. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1484.  71 
  1485.  72 def __call__(self, *args, **kwargs):
  1486. ---> 73 return self.f(*args, **kwargs)
  1487.  74 
  1488.  75 if not py3compat.PY3:
  1489.  
  1490. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1491.  179 args = ipython.unzip_args(args)
  1492.  180 with _setup_logging(args) as config:
  1493. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1494.  182 
  1495.  183 @require(alignprep)
  1496.  
  1497. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1498.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1499.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1500. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1501.  113 data = _add_supplemental_bams(data)
  1502.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1503.  
  1504. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1505.  62 else:
  1506.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1507. ---> 64 names, align_dir, data)
  1508.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1509.  66 if not data.get("align_split"):
  1510.  
  1511. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1512.  115 config = data["config"]
  1513.  116 align_fn = TOOLS[aligner].align_fn
  1514. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1515.  118 # handle align functions that update the main data dictionary in place
  1516.  119 if isinstance(out, dict):
  1517.  
  1518. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1519.  145 else:
  1520.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1521. --> 147 names, rg_info, data)
  1522.  148 data["work_bam"] = out_file
  1523.  149 return data
  1524.  
  1525. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1526.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1527.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1528. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1529.  158 return out_file
  1530.  159 
  1531.  
  1532. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1533.  19 try:
  1534.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1535. ---> 21 _do_run(cmd, checks, log_stdout)
  1536.  22 except:
  1537.  23 diagnostics.end_cmd(cmd_id, False)
  1538.  
  1539. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1540.  93 s.communicate()
  1541.  94 s.stdout.close()
  1542. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1543.  96 else:
  1544.  97 break
  1545.  
  1546. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 120000001 140000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 120000001 140000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f14153ed-58d9-4a5a-9ed6-d1f02a521533/tmpOXeBPn/NA12878-1-sort-120000001_140000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0e4f2576-aa97-4404-9f84-2c9f77b1e7f3/tmpzy52Mp/NA12878-1-sort-120000001_140000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/8bb544a1-303b-455b-9ebf-63c52f86c6af/tmpKHmrws/NA12878-1-sort-120000001_140000000.bam /dev/stdin
  1547. samblaster: Version 0.1.22
  1548. samblaster: Inputting from stdin
  1549. samblaster: Outputting to stdout
  1550. samblaster: Opening /dev/fd/62 for write.
  1551. samblaster: Opening /dev/fd/63 for write.
  1552. [M::mem_pestat] skip orientation FF as there are not enough pairs
  1553. [M::mem_pestat] skip orientation FR as there are not enough pairs
  1554. [M::mem_pestat] skip orientation RF as there are not enough pairs
  1555. [M::mem_pestat] skip orientation RR as there are not enough pairs
  1556. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20705:113542", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  1557.  
  1558. [mem_sam_pe] [mem_sam_pe] [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:20606:113544", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  1559.  
  1560. [mem_sam_pe] paired reads have different names: "HWI-ST1124:106:C15APACXX:1:2201:21059:113535", "HWI-ST1124:106:C15APACXX:1:1101:1469:2170"
  1561.  
  1562. [mem_sam_pe] samblaster: Loaded 84 header sequence entries.
  1563. ' returned non-zero exit status 1
  1564. cat: write error: Broken pipe
  1565. 2016-07-28 00:27:20.810 [IPEngineApp] Exception in apply request:
  1566. 
  1567. CalledProcessErrorTraceback (most recent call last)
  1568. <string> in <module>()
  1569.  
  1570. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1571.  71 
  1572.  72 def __call__(self, *args, **kwargs):
  1573. ---> 73 return self.f(*args, **kwargs)
  1574.  74 
  1575.  75 if not py3compat.PY3:
  1576.  
  1577. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1578.  179 args = ipython.unzip_args(args)
  1579.  180 with _setup_logging(args) as config:
  1580. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1581.  182 
  1582.  183 @require(alignprep)
  1583.  
  1584. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1585.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1586.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1587. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1588.  113 data = _add_supplemental_bams(data)
  1589.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1590.  
  1591. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1592.  62 else:
  1593.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1594. ---> 64 names, align_dir, data)
  1595.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1596.  66 if not data.get("align_split"):
  1597.  
  1598. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1599.  115 config = data["config"]
  1600.  116 align_fn = TOOLS[aligner].align_fn
  1601. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1602.  118 # handle align functions that update the main data dictionary in place
  1603.  119 if isinstance(out, dict):
  1604.  
  1605. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1606.  145 else:
  1607.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1608. --> 147 names, rg_info, data)
  1609.  148 data["work_bam"] = out_file
  1610.  149 return data
  1611.  
  1612. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1613.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1614.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1615. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1616.  158 return out_file
  1617.  159 
  1618.  
  1619. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1620.  19 try:
  1621.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1622. ---> 21 _do_run(cmd, checks, log_stdout)
  1623.  22 except:
  1624.  23 diagnostics.end_cmd(cmd_id, False)
  1625.  
  1626. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1627.  93 s.communicate()
  1628.  94 s.stdout.close()
  1629. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1630.  96 else:
  1631.  97 break
  1632.  
  1633. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 60000001 80000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 60000001 80000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/011de5d7-b154-41df-bb14-2949bf5eba97/tmpeVj0HD/NA12878-1-sort-60000001_80000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/7d11710d-a234-4731-93e4-41908fb6aa72/tmpe22_UI/NA12878-1-sort-60000001_80000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/12f5566d-0ffc-4e8c-8585-082cf53fca86/tmpmAAwY2/NA12878-1-sort-60000001_80000000.bam /dev/stdin
  1634. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  1635. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  1636. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  1637. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  1638. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  1639. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  1640. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  1641. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  1642. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  1643. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  1644. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  1645. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  1646. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  1647. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  1648. duplicating @RG line NA12878-1
  1649. duplicating @PG line bwa
  1650. duplicating @SQ line 1
  1651. duplicating @SQ line 2
  1652. duplicating @SQ line 3
  1653. duplicating @SQ line 4
  1654. duplicating @SQ line 5
  1655. duplicating @SQ line 6
  1656. duplicating @SQ line 7
  1657. duplicating @SQ line 8
  1658. duplicating @SQ line 9
  1659. duplicating @SQ line 10
  1660. duplicating @SQ line 11
  1661. duplicating @SQ line 12
  1662. duplicating @SQ line 13
  1663. duplicating @SQ line 14
  1664. duplicating @SQ line 15
  1665. duplicating @SQ line 16
  1666. duplicating @SQ line 17
  1667. duplicating @SQ line 18
  1668. duplicating @SQ line 19
  1669. duplicating @SQ line 20
  1670. duplicating @SQ line 21
  1671. duplicating @SQ line 22
  1672. duplicating @SQ line X
  1673. duplicating @SQ line Y
  1674. duplicating @SQ line MT
  1675. duplicating @SQ line GL000207.1
  1676. duplicating @SQ line GL000226.1
  1677. duplicating @SQ line GL000229.1
  1678. duplicating @SQ line GL000231.1
  1679. duplicating @SQ line GL000210.1
  1680. duplicating @SQ line GL000239.1
  1681. duplicating @SQ line GL000235.1
  1682. duplicating @SQ line GL000201.1
  1683. duplicating @SQ line GL000247.1
  1684. duplicating @SQ line GL000245.1
  1685. duplicating @SQ line GL000197.1
  1686. duplicating @SQ line GL000203.1
  1687. duplicating @SQ line GL000246.1
  1688. duplicating @SQ line GL000249.1
  1689. duplicating @SQ line GL000196.1
  1690. duplicating @SQ line GL000248.1
  1691. duplicating @SQ line GL000244.1
  1692. duplicating @SQ line GL000238.1
  1693. duplicating @SQ line GL000202.1
  1694. duplicating @SQ line GL000234.1
  1695. duplicating @SQ line GL000232.1
  1696. duplicating @SQ line GL000206.1
  1697. duplicating @SQ line GL000240.1
  1698. duplicating @SQ line GL000236.1
  1699. duplicating @SQ line GL000241.1
  1700. duplicating @SQ line GL000243.1
  1701. duplicating @SQ line GL000242.1
  1702. duplicating @SQ line GL000230.1
  1703. duplicating @SQ line GL000237.1
  1704. duplicating @SQ line GL000233.1
  1705. duplicating @SQ line GL000204.1
  1706. duplicating @SQ line GL000198.1
  1707. duplicating @SQ line GL000208.1
  1708. duplicating @SQ line GL000191.1
  1709. duplicating @SQ line GL000227.1
  1710. duplicating @SQ line GL000228.1
  1711. duplicating @SQ line GL000214.1
  1712. duplicating @SQ line GL000221.1
  1713. duplicating @SQ line GL000209.1
  1714. duplicating @SQ line GL000218.1
  1715. duplicating @SQ line GL000220.1
  1716. duplicating @SQ line GL000213.1
  1717. duplicating @SQ line GL000211.1
  1718. duplicating @SQ line GL000199.1
  1719. duplicating @SQ line GL000217.1
  1720. duplicating @SQ line GL000216.1
  1721. duplicating @SQ line GL000215.1
  1722. duplicating @SQ line GL000205.1
  1723. duplicating @SQ line GL000219.1
  1724. duplicating @SQ line GL000224.1
  1725. duplicating @SQ line GL000223.1
  1726. duplicating @SQ line GL000195.1
  1727. duplicating @SQ line GL000212.1
  1728. duplicating @SQ line GL000222.1
  1729. duplicating @SQ line GL000200.1
  1730. duplicating @SQ line GL000193.1
  1731. duplicating @SQ line GL000194.1
  1732. duplicating @SQ line GL000225.1
  1733. duplicating @SQ line GL000192.1
  1734. ' returned non-zero exit status 1
  1735. cat: write error: Broken pipe
  1736. 2016-07-28 00:27:42.892 [IPEngineApp] Exception in apply request:
  1737. 
  1738. CalledProcessErrorTraceback (most recent call last)
  1739. <string> in <module>()
  1740.  
  1741. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1742.  71 
  1743.  72 def __call__(self, *args, **kwargs):
  1744. ---> 73 return self.f(*args, **kwargs)
  1745.  74 
  1746.  75 if not py3compat.PY3:
  1747.  
  1748. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1749.  179 args = ipython.unzip_args(args)
  1750.  180 with _setup_logging(args) as config:
  1751. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1752.  182 
  1753.  183 @require(alignprep)
  1754.  
  1755. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1756.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1757.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1758. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1759.  113 data = _add_supplemental_bams(data)
  1760.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1761.  
  1762. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1763.  62 else:
  1764.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1765. ---> 64 names, align_dir, data)
  1766.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1767.  66 if not data.get("align_split"):
  1768.  
  1769. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1770.  115 config = data["config"]
  1771.  116 align_fn = TOOLS[aligner].align_fn
  1772. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1773.  118 # handle align functions that update the main data dictionary in place
  1774.  119 if isinstance(out, dict):
  1775.  
  1776. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1777.  145 else:
  1778.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1779. --> 147 names, rg_info, data)
  1780.  148 data["work_bam"] = out_file
  1781.  149 return data
  1782.  
  1783. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1784.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1785.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1786. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1787.  158 return out_file
  1788.  159 
  1789.  
  1790. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1791.  19 try:
  1792.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1793. ---> 21 _do_run(cmd, checks, log_stdout)
  1794.  22 except:
  1795.  23 diagnostics.end_cmd(cmd_id, False)
  1796.  
  1797. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1798.  93 s.communicate()
  1799.  94 s.stdout.close()
  1800. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1801.  96 else:
  1802.  97 break
  1803.  
  1804. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 100000001 120000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 100000001 120000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/a6d6fcb9-d3a4-4778-b984-b0c9fe8b9c7c/tmpiekIbN/NA12878-1-sort-100000001_120000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/da518b93-a723-4ae6-9c67-6b32e4bbf239/tmpbgWYqv/NA12878-1-sort-100000001_120000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01ccd89d-561f-4238-8b3b-4f2e34fb548f/tmpfNPArL/NA12878-1-sort-100000001_120000000.bam /dev/stdin
  1805. duplicating @SQ line GL000199.1
  1806. duplicating @SQ line GL000217.1
  1807. duplicating @SQ line GL000216.1
  1808. duplicating @SQ line GL000215.1
  1809. duplicating @SQ line GL000205.1
  1810. duplicating @SQ line GL000219.1
  1811. duplicating @SQ line GL000224.1
  1812. duplicating @SQ line GL000223.1
  1813. duplicating @SQ line GL000195.1
  1814. duplicating @SQ line GL000212.1
  1815. duplicating @SQ line GL000222.1
  1816. duplicating @SQ line GL000200.1
  1817. duplicating @SQ line GL000193.1
  1818. duplicating @SQ line GL000194.1
  1819. duplicating @SQ line GL000225.1
  1820. duplicating @SQ line GL000192.1
  1821. duplicating @SQ line 1
  1822. duplicating @SQ line 2
  1823. duplicating @SQ line 3
  1824. duplicating @SQ line 4
  1825. duplicating @SQ line 5
  1826. duplicating @SQ line 6
  1827. duplicating @SQ line 7
  1828. duplicating @SQ line 8
  1829. duplicating @SQ line 9
  1830. duplicating @SQ line 10
  1831. duplicating @SQ line 11
  1832. duplicating @SQ line 12
  1833. duplicating @SQ line 13
  1834. duplicating @SQ line 14
  1835. duplicating @SQ line 15
  1836. duplicating @SQ line 16
  1837. duplicating @SQ line 17
  1838. duplicating @SQ line 18
  1839. duplicating @SQ line 19
  1840. duplicating @SQ line 20
  1841. duplicating @SQ line 21
  1842. duplicating @SQ line 22
  1843. duplicating @SQ line X
  1844. duplicating @SQ line Y
  1845. duplicating @SQ line MT
  1846. duplicating @SQ line GL000207.1
  1847. duplicating @SQ line GL000226.1
  1848. duplicating @SQ line GL000229.1
  1849. duplicating @SQ line GL000231.1
  1850. duplicating @SQ line GL000210.1
  1851. duplicating @SQ line GL000239.1
  1852. duplicating @SQ line GL000235.1
  1853. duplicating @SQ line GL000201.1
  1854. duplicating @SQ line GL000247.1
  1855. duplicating @SQ line GL000245.1
  1856. duplicating @SQ line GL000197.1
  1857. duplicating @SQ line GL000203.1
  1858. duplicating @SQ line GL000246.1
  1859. duplicating @SQ line GL000249.1
  1860. duplicating @SQ line GL000196.1
  1861. duplicating @SQ line GL000248.1
  1862. duplicating @SQ line GL000244.1
  1863. duplicating @SQ line GL000238.1
  1864. duplicating @SQ line GL000202.1
  1865. duplicating @SQ line GL000234.1
  1866. duplicating @SQ line GL000232.1
  1867. duplicating @SQ line GL000206.1
  1868. duplicating @SQ line GL000240.1
  1869. duplicating @SQ line GL000236.1
  1870. duplicating @SQ line GL000241.1
  1871. duplicating @SQ line GL000243.1
  1872. duplicating @SQ line GL000242.1
  1873. duplicating @SQ line GL000230.1
  1874. duplicating @SQ line GL000237.1
  1875. duplicating @SQ line GL000233.1
  1876. duplicating @SQ line GL000204.1
  1877. duplicating @SQ line GL000198.1
  1878. duplicating @SQ line GL000208.1
  1879. duplicating @SQ line GL000191.1
  1880. duplicating @SQ line GL000227.1
  1881. duplicating @SQ line GL000228.1
  1882. duplicating @SQ line GL000214.1
  1883. duplicating @SQ line GL000221.1
  1884. duplicating @SQ line GL000209.1
  1885. duplicating @SQ line GL000218.1
  1886. duplicating @SQ line GL000220.1
  1887. duplicating @SQ line GL000213.1
  1888. duplicating @SQ line GL000211.1
  1889. duplicating @SQ line GL000199.1
  1890. duplicating @SQ line GL000217.1
  1891. duplicating @SQ line GL000216.1
  1892. duplicating @SQ line GL000215.1
  1893. duplicating @SQ line GL000205.1
  1894. duplicating @SQ line GL000219.1
  1895. duplicating @SQ line GL000224.1
  1896. duplicating @SQ line GL000223.1
  1897. duplicating @SQ line GL000195.1
  1898. duplicating @SQ line GL000212.1
  1899. duplicating @SQ line GL000222.1
  1900. duplicating @SQ line GL000200.1
  1901. duplicating @SQ line GL000193.1
  1902. duplicating @SQ line GL000194.1
  1903. duplicating @SQ line GL000225.1
  1904. duplicating @SQ line GL000192.1
  1905. ' returned non-zero exit status 1
  1906. cat: write error: Broken pipe
  1907. 2016-07-28 00:28:05.672 [IPEngineApp] Exception in apply request:
  1908. 
  1909. CalledProcessErrorTraceback (most recent call last)
  1910. <string> in <module>()
  1911.  
  1912. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  1913.  71 
  1914.  72 def __call__(self, *args, **kwargs):
  1915. ---> 73 return self.f(*args, **kwargs)
  1916.  74 
  1917.  75 if not py3compat.PY3:
  1918.  
  1919. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  1920.  179 args = ipython.unzip_args(args)
  1921.  180 with _setup_logging(args) as config:
  1922. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  1923.  182 
  1924.  183 @require(alignprep)
  1925.  
  1926. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  1927.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  1928.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  1929. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  1930.  113 data = _add_supplemental_bams(data)
  1931.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  1932.  
  1933. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  1934.  62 else:
  1935.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  1936. ---> 64 names, align_dir, data)
  1937.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  1938.  66 if not data.get("align_split"):
  1939.  
  1940. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  1941.  115 config = data["config"]
  1942.  116 align_fn = TOOLS[aligner].align_fn
  1943. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  1944.  118 # handle align functions that update the main data dictionary in place
  1945.  119 if isinstance(out, dict):
  1946.  
  1947. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  1948.  145 else:
  1949.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  1950. --> 147 names, rg_info, data)
  1951.  148 data["work_bam"] = out_file
  1952.  149 return data
  1953.  
  1954. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  1955.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  1956.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  1957. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  1958.  158 return out_file
  1959.  159 
  1960.  
  1961. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  1962.  19 try:
  1963.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  1964. ---> 21 _do_run(cmd, checks, log_stdout)
  1965.  22 except:
  1966.  23 diagnostics.end_cmd(cmd_id, False)
  1967.  
  1968. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  1969.  93 s.communicate()
  1970.  94 s.stdout.close()
  1971. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  1972.  96 else:
  1973.  97 break
  1974.  
  1975. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-1\tPL:illumina\tPU:NA12878-1\tSM:NA12878-1' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 80000001 100000000) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 80000001 100000000) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/0445b705-698a-4810-8f4c-166804830938/tmpE9lDEw/NA12878-1-sort-80000001_100000000-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/71945eff-862b-4166-a0c7-72bc6f9b50ca/tmp3xwsIG/NA12878-1-sort-80000001_100000000-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/f36686cb-b5c9-4b34-92c0-6645e89529f8/tmpiF_JQm/NA12878-1-sort-80000001_100000000.bam /dev/stdin
  1976. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  1977. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  1978. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  1979. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  1980. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  1981. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  1982. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  1983. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  1984. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  1985. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  1986. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  1987. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  1988. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  1989. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  1990. duplicating @RG line NA12878-1
  1991. duplicating @PG line bwa
  1992. duplicating @SQ line 1
  1993. duplicating @SQ line 2
  1994. duplicating @SQ line 3
  1995. duplicating @SQ line 4
  1996. duplicating @SQ line 5
  1997. duplicating @SQ line 6
  1998. duplicating @SQ line 7
  1999. duplicating @SQ line 8
  2000. duplicating @SQ line 9
  2001. duplicating @SQ line 10
  2002. duplicating @SQ line 11
  2003. duplicating @SQ line 12
  2004. duplicating @SQ line 13
  2005. duplicating @SQ line 14
  2006. duplicating @SQ line 15
  2007. duplicating @SQ line 16
  2008. duplicating @SQ line 17
  2009. duplicating @SQ line 18
  2010. duplicating @SQ line 19
  2011. duplicating @SQ line 20
  2012. duplicating @SQ line 21
  2013. duplicating @SQ line 22
  2014. duplicating @SQ line X
  2015. duplicating @SQ line Y
  2016. duplicating @SQ line MT
  2017. duplicating @SQ line GL000207.1
  2018. duplicating @SQ line GL000226.1
  2019. duplicating @SQ line GL000229.1
  2020. duplicating @SQ line GL000231.1
  2021. duplicating @SQ line GL000210.1
  2022. duplicating @SQ line GL000239.1
  2023. duplicating @SQ line GL000235.1
  2024. duplicating @SQ line GL000201.1
  2025. duplicating @SQ line GL000247.1
  2026. duplicating @SQ line GL000245.1
  2027. duplicating @SQ line GL000197.1
  2028. duplicating @SQ line GL000203.1
  2029. duplicating @SQ line GL000246.1
  2030. duplicating @SQ line GL000249.1
  2031. duplicating @SQ line GL000196.1
  2032. duplicating @SQ line GL000248.1
  2033. duplicating @SQ line GL000244.1
  2034. duplicating @SQ line GL000238.1
  2035. duplicating @SQ line GL000202.1
  2036. duplicating @SQ line GL000234.1
  2037. duplicating @SQ line GL000232.1
  2038. duplicating @SQ line GL000206.1
  2039. duplicating @SQ line GL000240.1
  2040. duplicating @SQ line GL000236.1
  2041. duplicating @SQ line GL000241.1
  2042. duplicating @SQ line GL000243.1
  2043. duplicating @SQ line GL000242.1
  2044. duplicating @SQ line GL000230.1
  2045. duplicating @SQ line GL000237.1
  2046. duplicating @SQ line GL000233.1
  2047. duplicating @SQ line GL000204.1
  2048. duplicating @SQ line GL000198.1
  2049. duplicating @SQ line GL000208.1
  2050. duplicating @SQ line GL000191.1
  2051. duplicating @SQ line GL000227.1
  2052. duplicating @SQ line GL000228.1
  2053. duplicating @SQ line GL000214.1
  2054. duplicating @SQ line GL000221.1
  2055. duplicating @SQ line GL000209.1
  2056. duplicating @SQ line GL000218.1
  2057. duplicating @SQ line GL000220.1
  2058. duplicating @SQ line GL000213.1
  2059. duplicating @SQ line GL000211.1
  2060. duplicating @SQ line GL000199.1
  2061. duplicating @SQ line GL000217.1
  2062. duplicating @SQ line GL000216.1
  2063. duplicating @SQ line GL000215.1
  2064. duplicating @SQ line GL000205.1
  2065. duplicating @SQ line GL000219.1
  2066. duplicating @SQ line GL000224.1
  2067. duplicating @SQ line GL000223.1
  2068. duplicating @SQ line GL000195.1
  2069. duplicating @SQ line GL000212.1
  2070. duplicating @SQ line GL000222.1
  2071. duplicating @SQ line GL000200.1
  2072. duplicating @SQ line GL000193.1
  2073. duplicating @SQ line GL000194.1
  2074. duplicating @SQ line GL000225.1
  2075. duplicating @SQ line GL000192.1
  2076. ' returned non-zero exit status 1
  2077. cat: write error: Broken pipe
  2078. 2016-07-28 00:28:53.469 [IPEngineApp] Exception in apply request:
  2079. 
  2080. CalledProcessErrorTraceback (most recent call last)
  2081. <string> in <module>()
  2082.  
  2083. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/controller/dependency.pyc in __call__(self, *args, **kwargs)
  2084.  71 
  2085.  72 def __call__(self, *args, **kwargs):
  2086. ---> 73 return self.f(*args, **kwargs)
  2087.  74 
  2088.  75 if not py3compat.PY3:
  2089.  
  2090. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.pyc in process_alignment(*args)
  2091.  179 args = ipython.unzip_args(args)
  2092.  180 with _setup_logging(args) as config:
  2093. --> 181 return ipython.zip_args(apply(sample.process_alignment, *args))
  2094.  182 
  2095.  183 @require(alignprep)
  2096.  
  2097. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.pyc in process_alignment(data, alt_input)
  2098.  110 if fastq1 and objectstore.file_exists_or_remote(fastq1) and aligner:
  2099.  111 logger.info("Aligning lane %s with %s aligner" % (data["rgnames"]["lane"], aligner))
  2100. --> 112 data = align_to_sort_bam(fastq1, fastq2, aligner, data)
  2101.  113 data = _add_supplemental_bams(data)
  2102.  114 elif fastq1 and objectstore.file_exists_or_remote(fastq1) and fastq1.endswith(".bam"):
  2103.  
  2104. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in align_to_sort_bam(fastq1, fastq2, aligner, data)
  2105.  62 else:
  2106.  63 data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
  2107. ---> 64 names, align_dir, data)
  2108.  65 if data["work_bam"] and utils.file_exists(data["work_bam"]):
  2109.  66 if not data.get("align_split"):
  2110.  
  2111. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.pyc in _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names, align_dir, data)
  2112.  115 config = data["config"]
  2113.  116 align_fn = TOOLS[aligner].align_fn
  2114. --> 117 out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
  2115.  118 # handle align functions that update the main data dictionary in place
  2116.  119 if isinstance(out, dict):
  2117.  
  2118. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in align_pipe(fastq_file, pair_file, ref_file, names, align_dir, data)
  2119.  145 else:
  2120.  146 out_file = _align_mem(fastq_file, pair_file, ref_file, out_file,
  2121. --> 147 names, rg_info, data)
  2122.  148 data["work_bam"] = out_file
  2123.  149 return data
  2124.  
  2125. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.pyc in _align_mem(fastq_file, pair_file, ref_file, out_file, names, rg_info, data)
  2126.  155 cmd = "%s | %s" % (_get_bwa_mem_cmd(data, out_file, ref_file, fastq_file, pair_file), tobam_cl)
  2127.  156 do.run(cmd, "bwa mem alignment from fastq: %s" % names["sample"], None,
  2128. --> 157 [do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
  2129.  158 return out_file
  2130.  159 
  2131.  
  2132. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in run(cmd, descr, data, checks, region, log_error, log_stdout)
  2133.  19 try:
  2134.  20 logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
  2135. ---> 21 _do_run(cmd, checks, log_stdout)
  2136.  22 except:
  2137.  23 diagnostics.end_cmd(cmd_id, False)
  2138.  
  2139. /home/hofmann/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.pyc in _do_run(cmd, checks, log_stdout)
  2140.  93 s.communicate()
  2141.  94 s.stdout.close()
  2142. ---> 95 raise subprocess.CalledProcessError(exitcode, error_msg)
  2143.  96 else:
  2144.  97 break
  2145.  
  2146. CalledProcessError: Command 'set -o pipefail; /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/bwa mem -c 250 -M -t 16 -R '@RG\tID:NA12878-2\tPL:illumina\tPU:NA12878-2\tSM:NA12878-2' -v 1 /home/hofmann/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_1.fastq.gz 160000001 176313700) <(grabix grab /scratch/hofmann/projects/NA12878-exome-eval/work_cloud_dist/align_prep/NA12878-NGv3-LAB1360-A_2.fastq.gz 160000001 176313700) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-spl -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/01490ba2-57c3-42b9-a1cd-50145333b5f2/tmp1C0LJg/NA12878-2-sort-160000001_176313700-sr.bam /dev/stdin) --discordantFile >(/home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 682M -T /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-disc -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/ad8af680-18c4-49e8-84fe-0750516cce50/tmpYmIxfA/NA12878-2-sort-160000001_176313700-disc.bam /dev/stdin) | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /home/hofmann/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 682M --tmpdir /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700-sorttmp-full -o /scratch/hofmann/projects/NA12878-exome-eval/tmp/bcbiotx/08751093-9024-4609-9794-a31ef68c3151/tmpCzS63B/NA12878-2-sort-160000001_176313700.bam /dev/stdin
  2147. [W::sam_hdr_parse] duplicated sequence 'GL000216.1'
  2148. [W::sam_hdr_parse] duplicated sequence 'GL000215.1'
  2149. [W::sam_hdr_parse] duplicated sequence 'GL000205.1'
  2150. [W::sam_hdr_parse] duplicated sequence 'GL000219.1'
  2151. [W::sam_hdr_parse] duplicated sequence 'GL000224.1'
  2152. [W::sam_hdr_parse] duplicated sequence 'GL000223.1'
  2153. [W::sam_hdr_parse] duplicated sequence 'GL000195.1'
  2154. [W::sam_hdr_parse] duplicated sequence 'GL000212.1'
  2155. [W::sam_hdr_parse] duplicated sequence 'GL000222.1'
  2156. [W::sam_hdr_parse] duplicated sequence 'GL000200.1'
  2157. [W::sam_hdr_parse] duplicated sequence 'GL000193.1'
  2158. [W::sam_hdr_parse] duplicated sequence 'GL000194.1'
  2159. [W::sam_hdr_parse] duplicated sequence 'GL000225.1'
  2160. [W::sam_hdr_parse] duplicated sequence 'GL000192.1'
  2161. duplicating @RG line NA12878-2
  2162. duplicating @PG line bwa
  2163. duplicating @SQ line 1
  2164. duplicating @SQ line 2
  2165. duplicating @SQ line 3
  2166. duplicating @SQ line 4
  2167. duplicating @SQ line 5
  2168. duplicating @SQ line 6
  2169. duplicating @SQ line 7
  2170. duplicating @SQ line 8
  2171. duplicating @SQ line 9
  2172. duplicating @SQ line 10
  2173. duplicating @SQ line 11
  2174. duplicating @SQ line 12
  2175. duplicating @SQ line 13
  2176. duplicating @SQ line 14
  2177. duplicating @SQ line 15
  2178. duplicating @SQ line 16
  2179. duplicating @SQ line 17
  2180. duplicating @SQ line 18
  2181. duplicating @SQ line 19
  2182. duplicating @SQ line 20
  2183. duplicating @SQ line 21
  2184. duplicating @SQ line 22
  2185. duplicating @SQ line X
  2186. duplicating @SQ line Y
  2187. duplicating @SQ line MT
  2188. duplicating @SQ line GL000207.1
  2189. duplicating @SQ line GL000226.1
  2190. duplicating @SQ line GL000229.1
  2191. duplicating @SQ line GL000231.1
  2192. duplicating @SQ line GL000210.1
  2193. duplicating @SQ line GL000239.1
  2194. duplicating @SQ line GL000235.1
  2195. duplicating @SQ line GL000201.1
  2196. duplicating @SQ line GL000247.1
  2197. duplicating @SQ line GL000245.1
  2198. duplicating @SQ line GL000197.1
  2199. duplicating @SQ line GL000203.1
  2200. duplicating @SQ line GL000246.1
  2201. duplicating @SQ line GL000249.1
  2202. duplicating @SQ line GL000196.1
  2203. duplicating @SQ line GL000248.1
  2204. duplicating @SQ line GL000244.1
  2205. duplicating @SQ line GL000238.1
  2206. duplicating @SQ line GL000202.1
  2207. duplicating @SQ line GL000234.1
  2208. duplicating @SQ line GL000232.1
  2209. duplicating @SQ line GL000206.1
  2210. duplicating @SQ line GL000240.1
  2211. duplicating @SQ line GL000236.1
  2212. duplicating @SQ line GL000241.1
  2213. duplicating @SQ line GL000243.1
  2214. duplicating @SQ line GL000242.1
  2215. duplicating @SQ line GL000230.1
  2216. duplicating @SQ line GL000237.1
  2217. duplicating @SQ line GL000233.1
  2218. duplicating @SQ line GL000204.1
  2219. duplicating @SQ line GL000198.1
  2220. duplicating @SQ line GL000208.1
  2221. duplicating @SQ line GL000191.1
  2222. duplicating @SQ line GL000227.1
  2223. duplicating @SQ line GL000228.1
  2224. duplicating @SQ line GL000214.1
  2225. duplicating @SQ line GL000221.1
  2226. duplicating @SQ line GL000209.1
  2227. duplicating @SQ line GL000218.1
  2228. duplicating @SQ line GL000220.1
  2229. duplicating @SQ line GL000213.1
  2230. duplicating @SQ line GL000211.1
  2231. duplicating @SQ line GL000199.1
  2232. duplicating @SQ line GL000217.1
  2233. duplicating @SQ line GL000216.1
  2234. duplicating @SQ line GL000215.1
  2235. duplicating @SQ line GL000205.1
  2236. duplicating @SQ line GL000219.1
  2237. duplicating @SQ line GL000224.1
  2238. duplicating @SQ line GL000223.1
  2239. duplicating @SQ line GL000195.1
  2240. duplicating @SQ line GL000212.1
  2241. duplicating @SQ line GL000222.1
  2242. duplicating @SQ line GL000200.1
  2243. duplicating @SQ line GL000193.1
  2244. duplicating @SQ line GL000194.1
  2245. duplicating @SQ line GL000225.1
  2246. duplicating @SQ line GL000192.1
  2247. ' returned non-zero exit status 1
  2248. slurmstepd: *** JOB 30513 ON spartan063 CANCELLED AT 2016-07-28T00:29:07 ***
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!