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  1. awk '{ if ($0 ~ "transcript_id") print $0; else print $0" transcript_id "";"; }' Homo_sapiens.GRCh38.gtf | gtf2bed - > $Homo_sapiens.GRCh38.bed
  2.  
  3. Reading reference bed file: /rst1/2017-0205_illuminaseq/data/references/Reference_Genomes/GRCh38.95/Homo_sapiens.GRCh38.87.bed ... Traceback (most recent call last):
  4. File "/rst1/2017-0205_illuminaseq/tools/snakemake_conda_env/f4c16777/bin/junction_annotation.py", line 125, in <module>
  5. main()
  6. File "/rst1/2017-0205_illuminaseq/tools/snakemake_conda_env/f4c16777/bin/junction_annotation.py", line 109, in main
  7. obj.annotate_junction(outfile=options.output_prefix,refgene=options.ref_gene_model,min_intron=options.min_intron, q_cut = options.map_qual)
  8. File "/rst1/2017-0205_illuminaseq/tools/snakemake_conda_env/f4c16777/lib/python2.7/site-packages/qcmodule/SAM.py", line 3762, in annotate_junction
  9. exon_starts = map( int, fields[11].rstrip( ',n' ).split( ',' ) )
  10. ValueError: invalid literal for int() with base 10: 'gene_version'
  11.  
  12. 1 11868 12227 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
  13. 1 11868 14409 ENSG00000223972 . + havana gene . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_id "";
  14. 1 11868 14409 ENSG00000223972 . + havana transcript . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
  15. 1 12009 12057 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
  16. 1 12009 13670 ENSG00000223972 . + havana transcript . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
  17. 1 12178 12227 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
  18. 1 12612 12697 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
  19. 1 12612 12721 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
  20. 1 12974 13052 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
  21. 1 13220 13374 ENSG00000223972 . + havana exon . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
  22.  
  23. 1 11868 14409 ENST00000456328 0 + 11868 14409 0 3 359,109,1189, 0,744,1352, DDX11L1
  24. 1 12009 13670 ENST00000450305 0 + 12009 13670 0 6 48,49,85,78,154,218, 0,169,603,965,1211,1443, DDX11L1
  25. 1 17368 17436 ENST00000619216 0 - 17368 17436 0 1 68, 0, MIR6859-1
  26. 1 14403 29570 ENST00000488147 0 - 14403 29570 0 11 98,34,152,159,198,136,137,147,99,154,37, 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130, WASH7P
  27. 1 29553 31097 ENST00000473358 0 + 29553 31097 0 3 486,104,122, 0,1010,1422, MIR1302-2
  28. 1 30266 31109 ENST00000469289 0 + 30266 31109 0 2 401,134, 0,709, MIR1302-2
  29. 1 30365 30503 ENST00000607096 0 + 30365 30503 0 1 138, 0, MIR1302-2
  30. 1 34553 36081 ENST00000417324 0 - 34553 36081 0 3 621,205,361, 0,723,1167, FAM138A
  31. 1 35244 36073 ENST00000461467 0 - 35244 36073 0 2 237,353, 0,476, FAM138A
  32. 1 52472 53312 ENST00000606857 0 + 52472 53312 0 1 840, 0, OR4G4P
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