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  1. efloden 39987 0.0 0.0 129980 992 ? S 10:40 0:00 | \_ -bash /usr/share/univage/soldierantcluster/spool/node-hp0206/job_scripts/29787929
  2. efloden 39996 0.0 0.0 20044 1520 ? S 10:40 0:00 | \_ /bin/bash -c cd /nfs/users2/cn/efloden/projects/dpa-benchfam-100k/work/0a/2fd33a5b29bb4e67e79d3a7cd99b09; eval export CACHE_4_TCOFFEE="${TMPDIR:-/tmp}/.tcoffee/cache" export LOCKDIR_4_TCOFFEE="${TMPDIR:-/tmp}/.tcoffee/lock" export TMP_4_TCOFFEE="${TMPDIR:-/tmp}/.tcoffee/tmp" export DUMMY="$(mkdir -p $CACHE_4_TCOFFEE; mkdir -p $LOCKDIR_4_TCOFFEE; mkdir -p $TMP_4_TCOFFEE)" export PATH="/nfs/users2/cn/efloden/projects/dpa-benchfam-100k/bin:$PATH"; /bin/bash /nfs/users2/cn/efloden/projects/dpa-benchfam-100k/work/0a/2fd33a5b29bb4e67e79d3a7cd99b09/.command.run nxf_trace
  3. efloden 40126 0.0 0.0 20304 1860 ? S 10:40 0:00 | \_ /bin/bash /nfs/users2/cn/efloden/projects/dpa-benchfam-100k/work/0a/2fd33a5b29bb4e67e79d3a7cd99b09/.command.run nxf_trace
  4. efloden 40179 0.0 0.0 20048 1504 ? S 10:40 0:00 | \_ /bin/bash -ue /nfs/users2/cn/efloden/projects/dpa-benchfam-100k/work/0a/2fd33a5b29bb4e67e79d3a7cd99b09/.command.sh
  5. efloden 40203 0.1 0.8 1178308 1164936 ? S 10:40 0:05 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  6. efloden 47321 0.0 0.8 1182400 1168108 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  7. efloden 47659 0.0 0.0 4324 644 ? S 10:40 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473213669.pl one seq aln 2PARAM
  8. efloden 47768 0.0 0.0 20892 3348 ? S 10:40 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473213669.pl one seq aln 2PARAM
  9. efloden 48013 0.0 0.0 4324 640 ? S 10:40 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  10. efloden 48137 0.0 0.0 58904 18680 ? S 10:40 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  11. efloden 53880 0.1 0.0 170380 61884 ? Sl 10:40 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/backbone/backboneFt10ih.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/
  12. efloden 59424 0.0 0.0 194228 16580 ? Sl 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/backbone/backboneFt10ih.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/
  13. efloden 64029 0.0 0.0 66148 21400 ? S 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/backbone/backboneFt10ih.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/
  14. efloden 9247 0.0 0.0 4324 656 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/pastajob/tempHdxk66/step1/mincluster/r2/d2/tempmafft3B_Pnl/input.fasta
  15. efloden 9319 0.0 0.0 4716 1076 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/pastajob/tempHdxk66/step1/mincluster/r2/d2/tempmafft3B_Pnl/input.fasta
  16. efloden 11172 0.0 0.0 4716 736 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ejQUfU/pastaout/pastajob/tempHdxk66/step1/mincluster/r2/d2/tempmafft3B_Pnl/input.fasta
  17. efloden 40078 6.2 0.0 145840 23860 ? Sl 11:36 0:00 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/dvtditr -s 0.0 -C 1 -t 0 -F -l 2.7 -z 50 -b 62 -f -1.53 -Q 100.0 -h -0.123 -I 16 -X -p BAATARI2
  18. efloden 47350 0.0 0.8 1182268 1168076 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  19. efloden 34624 0.1 0.0 4324 644 ? S 11:36 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473503669.pl one seq aln 2PARAM
  20. efloden 34823 0.0 0.0 20892 3348 ? S 11:36 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473503669.pl one seq aln 2PARAM
  21. efloden 34982 0.0 0.0 4324 640 ? S 11:36 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  22. efloden 35062 1.5 0.0 58904 18528 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  23. efloden 37029 3.0 0.0 129640 19932 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/backbone/backbonezQuDYv.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/
  24. efloden 39467 0.0 0.0 194228 16580 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/backbone/backbonezQuDYv.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/
  25. efloden 40064 0.0 0.0 61892 17164 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/backbone/backbonezQuDYv.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/
  26. efloden 42438 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/pastajob/temphaBBjM/step0/mincluster/r0/d1/tempmafftwX_0Q6/input.fasta
  27. efloden 42499 0.0 0.0 4324 672 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/pastajob/temphaBBjM/step0/mincluster/r0/d1/tempmafftwX_0Q6/input.fasta
  28. efloden 42834 0.0 0.0 4324 112 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/pastajob/temphaBBjM/step0/mincluster/r0/d1/tempmafftwX_0Q6/input.fasta
  29. efloden 42865 0.0 0.0 4324 116 ? R 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/pastajob/temphaBBjM/step0/mincluster/r0/d1/tempmafftwX_0Q6/input.fasta
  30. efloden 42866 0.0 0.0 4324 116 ? R 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.A4SxoU/pastaout/pastajob/temphaBBjM/step0/mincluster/r0/d1/tempmafftwX_0Q6/input.fasta
  31. efloden 47394 0.0 0.8 1179124 1164940 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  32. efloden 24319 0.0 0.0 4324 644 ? S 10:42 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473943794.pl one seq aln 2PARAM
  33. efloden 24960 0.0 0.0 20892 3344 ? S 10:42 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497473943794.pl one seq aln 2PARAM
  34. efloden 25638 0.0 0.0 4324 640 ? S 10:42 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  35. efloden 25873 0.0 0.0 58908 18676 ? S 10:42 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  36. efloden 31631 0.1 0.0 166684 58244 ? Sl 10:42 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/backbone/backbonelhMnlj.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/
  37. efloden 35882 0.0 0.0 194224 16588 ? Sl 10:42 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/backbone/backbonelhMnlj.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/
  38. efloden 38627 0.0 0.0 64816 20052 ? S 10:42 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/backbone/backbonelhMnlj.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/
  39. efloden 21996 5.9 0.0 13900 7304 ? R 11:35 0:02 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/pastajob/tempEL1Zve/step2/mincluster/tempfasttreees2zsm/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/pastajob/tempEL1Zve/step2/mincluster/tempfasttreees2zsm/log /scratch/29787929.1.long-sl7/sepp/seq.aln.xsweLr/pastaout/pastajob/tempEL1Zve/step2/mincluster/tempfasttreees2zsm/input.fasta
  40. efloden 47436 0.0 0.8 1179760 1165576 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  41. efloden 64932 0.0 0.0 4324 640 ? S 11:17 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497474363794.pl one seq aln 2PARAM
  42. efloden 65148 0.0 0.0 20892 3348 ? S 11:17 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497474363794.pl one seq aln 2PARAM
  43. efloden 65435 0.0 0.0 4324 640 ? S 11:17 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  44. efloden 65505 0.0 0.0 58904 18688 ? S 11:17 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  45. efloden 2880 0.1 0.0 150484 40900 ? Sl 11:18 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/backbone/backboneddGZJP.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/
  46. efloden 6472 0.0 0.0 194216 16584 ? Sl 11:18 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/backbone/backboneddGZJP.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/
  47. efloden 8537 0.0 0.0 66228 21480 ? S 11:18 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/backbone/backboneddGZJP.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/
  48. efloden 25258 0.0 0.0 4324 652 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/pastajob/tempAvipVU/step0/mincluster/r4/d1/tempmafftnunRMn/input.fasta
  49. efloden 25318 0.0 0.0 4716 1080 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/pastajob/tempAvipVU/step0/mincluster/r4/d1/tempmafftnunRMn/input.fasta
  50. efloden 27068 0.0 0.0 4716 700 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.lcOYT9/pastaout/pastajob/tempAvipVU/step0/mincluster/r4/d1/tempmafftnunRMn/input.fasta
  51. efloden 27163 6.1 0.0 113168 6940 ? Sl 11:36 0:01 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign -u 0.0 -l 2.7 -C 1 -b 62 -g -0.100 -f -2.00 -Q 100.0 -h 0.1 -L
  52. efloden 47470 0.1 0.8 1183324 1169104 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  53. efloden 38789 0.2 0.0 4324 644 ? S 11:36 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497474703794.pl one seq aln 2PARAM
  54. efloden 39024 0.1 0.0 20892 3348 ? S 11:36 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497474703794.pl one seq aln 2PARAM
  55. efloden 39175 0.0 0.0 4324 636 ? S 11:36 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  56. efloden 39258 3.1 0.0 58904 18524 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  57. efloden 41568 5.3 0.0 47032 14880 ? R 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.yszYCC/backbone/backboneRRYK68.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.yszYCC/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.yszYCC/pastaout/
  58. efloden 47547 0.0 0.8 1181080 1166772 ? R 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  59. efloden 47622 0.0 0.8 1180348 1166088 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  60. efloden 13540 0.0 0.0 4324 644 ? S 11:35 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497476223794.pl one seq aln 2PARAM
  61. efloden 13793 0.0 0.0 20892 3344 ? S 11:35 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497476223794.pl one seq aln 2PARAM
  62. efloden 14039 0.0 0.0 4324 640 ? S 11:35 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  63. efloden 14128 0.4 0.0 58892 18524 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  64. efloden 16059 0.7 0.0 129932 20204 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/backbone/backbone3yhoga.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/
  65. efloden 18601 0.0 0.0 194228 16716 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/backbone/backbone3yhoga.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/
  66. efloden 19164 0.0 0.0 61892 17172 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/backbone/backbone3yhoga.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/
  67. efloden 42730 0.0 0.0 1391500 8960 ? Sl 11:36 0:00 | | | \_ java -Xmx1024m -jar /pasta-code/pasta/bin/opal.jar --in /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/pastajob/tempazdTJS/step1/mincluster/pw/r1d2_r0d2/tempopal0WX3Ht/1_U2X.fasta --in2 /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/pastajob/tempazdTJS/step1/mincluster/pw/r1d2_r0d2/tempopal0WX3Ht/2_U2X.fasta --out /scratch/29787929.1.long-sl7/sepp/seq.aln.17owrH/pastaout/pastajob/tempazdTJS/step1/mincluster/pw/r1d2_r0d2/tempopal0WX3Ht/out_rep.fasta --align_method profile
  68. efloden 47785 0.0 0.8 1179760 1165576 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  69. efloden 56643 0.0 0.0 4324 644 ? S 10:55 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497477853794.pl one seq aln 2PARAM
  70. efloden 56930 0.0 0.0 20892 3344 ? S 10:55 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497477853794.pl one seq aln 2PARAM
  71. efloden 57230 0.0 0.0 4324 640 ? S 10:55 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  72. efloden 57336 0.0 0.0 58908 18676 ? S 10:55 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  73. efloden 59770 0.1 0.0 171376 63512 ? Sl 10:55 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/backbone/backbonelb1TPA.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/
  74. efloden 62995 0.0 0.0 194228 16588 ? Sl 10:55 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/backbone/backbonelb1TPA.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/
  75. efloden 64793 0.0 0.0 66644 21816 ? S 10:55 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/backbone/backbonelb1TPA.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/
  76. efloden 42498 0.0 0.0 1645248 20352 ? Sl 11:36 0:00 | | | \_ java -Xmx1024m -jar /pasta-code/pasta/bin/opal.jar --in /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/pastajob/tempaUvPVp/step1/mincluster/pw/r4d2_r0d2/tempopalLpFi9w/1_U2X.fasta --in2 /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/pastajob/tempaUvPVp/step1/mincluster/pw/r4d2_r0d2/tempopalLpFi9w/2_U2X.fasta --out /scratch/29787929.1.long-sl7/sepp/seq.aln.WfGd93/pastaout/pastajob/tempaUvPVp/step1/mincluster/pw/r4d2_r0d2/tempopalLpFi9w/out_rep.fasta --align_method profile
  77. efloden 47912 0.0 0.8 1180008 1165824 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  78. efloden 43187 0.0 0.0 4324 644 ? S 11:30 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497479123794.pl one seq aln 2PARAM
  79. efloden 43454 0.0 0.0 20892 3348 ? S 11:30 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497479123794.pl one seq aln 2PARAM
  80. efloden 43653 0.0 0.0 4324 636 ? S 11:30 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  81. efloden 43735 0.0 0.0 58904 18676 ? S 11:30 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  82. efloden 45742 0.5 0.0 150460 40996 ? Sl 11:30 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/backbone/backboneTl2unT.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/
  83. efloden 47411 0.0 0.0 194228 16592 ? Sl 11:30 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/backbone/backboneTl2unT.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/
  84. efloden 48482 0.0 0.0 66404 21628 ? S 11:30 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/backbone/backboneTl2unT.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/
  85. efloden 48328 0.0 0.0 4324 656 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/pastajob/tempadt1CK/step0/mincluster/r2/d2/tempmafftuIUxxf/input.fasta
  86. efloden 48393 0.0 0.0 4716 1080 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/pastajob/tempadt1CK/step0/mincluster/r2/d2/tempmafftuIUxxf/input.fasta
  87. efloden 49879 0.0 0.0 4716 740 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.Y8_bNe/pastaout/pastajob/tempadt1CK/step0/mincluster/r2/d2/tempmafftuIUxxf/input.fasta
  88. efloden 23246 6.0 0.0 142272 20372 ? Sl 11:35 0:02 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/dvtditr -s 0.0 -C 1 -t 0 -F -l 2.7 -z 50 -b 62 -f -1.53 -Q 100.0 -h -0.123 -I 16 -X -p BAATARI2
  89. efloden 47996 0.0 0.8 1182400 1168108 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  90. efloden 48954 0.0 0.0 4324 644 ? S 10:40 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497479963669.pl one seq aln 2PARAM
  91. efloden 49254 0.0 0.0 20892 3344 ? S 10:40 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497479963669.pl one seq aln 2PARAM
  92. efloden 49650 0.0 0.0 4324 636 ? S 10:40 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  93. efloden 49807 0.0 0.0 58896 18684 ? S 10:40 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  94. efloden 53834 0.1 0.0 170296 61968 ? Sl 10:40 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/backbone/backbone5kEzm5.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/
  95. efloden 59336 0.0 0.0 194228 16584 ? Sl 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/backbone/backbone5kEzm5.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/
  96. efloden 64134 0.0 0.0 66380 21596 ? S 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/backbone/backbone5kEzm5.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/
  97. efloden 19961 0.0 0.0 4324 656 ? S 11:33 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/pastajob/temp357Vis/step1/mincluster/r2/d2/tempmafft4gEwoG/input.fasta
  98. efloden 20045 0.0 0.0 4716 1080 ? S 11:33 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/pastajob/temp357Vis/step1/mincluster/r2/d2/tempmafft4gEwoG/input.fasta
  99. efloden 21704 0.0 0.0 4716 740 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.698ApE/pastaout/pastajob/temp357Vis/step1/mincluster/r2/d2/tempmafft4gEwoG/input.fasta
  100. efloden 60136 6.1 0.0 146888 24044 ? Sl 11:35 0:05 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/dvtditr -s 0.0 -C 1 -t 0 -F -l 2.7 -z 50 -b 62 -f -1.53 -Q 100.0 -h -0.123 -I 16 -X -p BAATARI2
  101. efloden 48163 0.0 0.8 1181344 1167092 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  102. efloden 49271 0.0 0.0 4324 644 ? S 10:40 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497481633669.pl one seq aln 2PARAM
  103. efloden 49705 0.0 0.0 20892 3344 ? S 10:40 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497481633669.pl one seq aln 2PARAM
  104. efloden 50026 0.0 0.0 4324 640 ? S 10:40 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  105. efloden 50183 0.0 0.0 58904 18676 ? S 10:40 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  106. efloden 54160 0.1 0.0 175668 67428 ? Sl 10:40 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/backbone/backboneF37aIC.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/
  107. efloden 59677 0.0 0.0 194224 16596 ? Sl 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/backbone/backboneF37aIC.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/
  108. efloden 63289 0.0 0.0 64952 20324 ? S 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/backbone/backboneF37aIC.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/
  109. efloden 7744 6.1 0.0 14244 7776 ? R 11:35 0:03 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/pastajob/tempUIN8EN/step2/mincluster/tempfasttreelqRNOy/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/pastajob/tempUIN8EN/step2/mincluster/tempfasttreelqRNOy/log /scratch/29787929.1.long-sl7/sepp/seq.aln.Y4t445/pastaout/pastajob/tempUIN8EN/step2/mincluster/tempfasttreelqRNOy/input.fasta
  110. efloden 48362 0.0 0.8 1182400 1168108 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  111. efloden 49756 0.0 0.0 4324 644 ? S 10:40 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497483623669.pl one seq aln 2PARAM
  112. efloden 50129 0.0 0.0 20892 3348 ? S 10:40 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497483623669.pl one seq aln 2PARAM
  113. efloden 50517 0.0 0.0 4324 640 ? S 10:40 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  114. efloden 50641 0.0 0.0 58904 18680 ? S 10:40 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  115. efloden 54819 0.0 0.0 155032 47020 ? Sl 10:40 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/backbone/backboneNjCCGw.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/
  116. efloden 60482 0.0 0.0 194216 16584 ? Sl 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/backbone/backboneNjCCGw.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/
  117. efloden 64803 0.0 0.0 66608 21772 ? S 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/backbone/backboneNjCCGw.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/
  118. efloden 61995 6.1 0.0 22704 16268 ? R 11:23 0:46 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/pastajob/tempWN0KYh/step0/mincluster/tempfasttreehXJukr/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/pastajob/tempWN0KYh/step0/mincluster/tempfasttreehXJukr/log /scratch/29787929.1.long-sl7/sepp/seq.aln.8fS0uE/pastaout/pastajob/tempWN0KYh/step0/mincluster/tempfasttreehXJukr/input.fasta
  119. efloden 48520 0.1 0.8 1180936 1166752 ? S 10:40 0:03 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  120. efloden 38787 0.0 0.0 4324 644 ? S 11:26 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497485203669.pl one seq aln 2PARAM
  121. efloden 38992 0.0 0.0 20892 3348 ? S 11:26 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497485203669.pl one seq aln 2PARAM
  122. efloden 39169 0.0 0.0 4324 640 ? S 11:26 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  123. efloden 39256 0.0 0.0 58892 18684 ? S 11:26 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  124. efloden 41012 0.1 0.0 135268 25556 ? Sl 11:26 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/backbone/backboneAspOMF.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/
  125. efloden 43406 0.0 0.0 194228 16580 ? Sl 11:26 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/backbone/backboneAspOMF.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/
  126. efloden 45239 0.0 0.0 66240 21540 ? S 11:26 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/backbone/backboneAspOMF.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/
  127. efloden 15095 6.1 0.0 20196 13848 ? R 11:27 0:32 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -log /scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/pastajob/tempN2wIdU/init_tree/tempfasttreeEkr4Pz/log /scratch/29787929.1.long-sl7/sepp/seq.aln.zetKvI/pastaout/pastajob/tempN2wIdU/init_tree/tempfasttreeEkr4Pz/input.fasta
  128. efloden 48750 0.1 0.8 1181424 1167112 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  129. efloden 26448 0.0 0.0 4324 644 ? S 11:22 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497487503669.pl one seq aln 2PARAM
  130. efloden 26733 0.0 0.0 20892 3344 ? S 11:22 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497487503669.pl one seq aln 2PARAM
  131. efloden 27014 0.0 0.0 4324 640 ? S 11:22 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  132. efloden 27133 0.0 0.0 58892 18672 ? S 11:22 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  133. efloden 29624 0.4 0.0 162788 53948 ? Sl 11:23 0:03 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/backbone/backboneFdHME9.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/
  134. efloden 32229 0.0 0.0 194228 16556 ? Sl 11:23 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/backbone/backboneFdHME9.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/
  135. efloden 33357 0.0 0.0 64672 19984 ? S 11:23 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/backbone/backboneFdHME9.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/
  136. efloden 33591 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/pastajob/temp9PNhJJ/step2/mincluster/r2/d2/tempmafftepvdCW/input.fasta
  137. efloden 33632 0.0 0.0 4716 1080 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/pastajob/temp9PNhJJ/step2/mincluster/r2/d2/tempmafftepvdCW/input.fasta
  138. efloden 34885 0.0 0.0 4716 700 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.TxanTg/pastaout/pastajob/temp9PNhJJ/step2/mincluster/r2/d2/tempmafftepvdCW/input.fasta
  139. efloden 35048 6.1 0.0 113128 5116 ? Sl 11:36 0:00 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign -u 0.0 -l 2.7 -C 1 -b 62 -g -0.100 -f -2.00 -Q 100.0 -h 0.1 -L
  140. efloden 48996 0.1 0.8 1181688 1167484 ? S 10:40 0:03 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  141. efloden 15364 0.0 0.0 4324 644 ? S 11:35 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497489963669.pl one seq aln 2PARAM
  142. efloden 15561 0.0 0.0 20892 3348 ? S 11:35 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497489963669.pl one seq aln 2PARAM
  143. efloden 15711 0.0 0.0 4324 640 ? S 11:35 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  144. efloden 15803 0.4 0.0 58892 18536 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  145. efloden 18164 0.7 0.0 129912 20276 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/backbone/backbonezopuEu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/
  146. efloden 20364 0.0 0.0 196280 16740 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/backbone/backbonezopuEu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/
  147. efloden 20807 0.0 0.0 62028 17308 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/backbone/backbonezopuEu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/
  148. efloden 41272 8.6 0.0 2110532 33596 ? Sl 11:36 0:00 | | | \_ java -Xmx1024m -jar /pasta-code/pasta/bin/opal.jar --in /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/pastajob/tempaNo_Eq/step0/mincluster/pw/r1d2_r0d2/tempopalEHkPzU/1_U2X.fasta --in2 /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/pastajob/tempaNo_Eq/step0/mincluster/pw/r1d2_r0d2/tempopalEHkPzU/2_U2X.fasta --out /scratch/29787929.1.long-sl7/sepp/seq.aln.IjaTDz/pastaout/pastajob/tempaNo_Eq/step0/mincluster/pw/r1d2_r0d2/tempopalEHkPzU/out_rep.fasta --align_method profile
  149. efloden 49229 0.0 0.8 1180860 1166648 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  150. efloden 41461 0.6 0.0 4324 644 ? S 11:36 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497492293794.pl one seq aln 2PARAM
  151. efloden 41664 0.5 0.0 20892 3348 ? S 11:36 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497492293794.pl one seq aln 2PARAM
  152. efloden 41831 0.0 0.0 4324 640 ? S 11:36 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  153. efloden 41914 6.0 0.0 42620 12292 ? R 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  154. efloden 49503 0.0 0.8 1180200 1166016 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  155. efloden 1855 0.0 0.0 4324 644 ? S 10:59 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497495033669.pl one seq aln 2PARAM
  156. efloden 2270 0.0 0.0 20892 3348 ? S 10:59 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497495033669.pl one seq aln 2PARAM
  157. efloden 2629 0.0 0.0 4324 640 ? S 10:59 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  158. efloden 2738 0.0 0.0 58892 18680 ? S 10:59 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  159. efloden 6007 0.1 0.0 173660 66124 ? Sl 10:59 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/backbone/backbonesK3_KQ.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/
  160. efloden 9354 0.0 0.0 194228 16572 ? Sl 10:59 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/backbone/backbonesK3_KQ.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/
  161. efloden 11913 0.0 0.0 66648 21816 ? S 10:59 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/backbone/backbonesK3_KQ.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/
  162. efloden 38650 6.1 0.0 16328 9864 ? R 11:34 0:07 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/pastajob/templkBmdC/step1/mincluster/tempfasttreeMlLVik/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/pastajob/templkBmdC/step1/mincluster/tempfasttreeMlLVik/log /scratch/29787929.1.long-sl7/sepp/seq.aln.hrsTX_/pastaout/pastajob/templkBmdC/step1/mincluster/tempfasttreeMlLVik/input.fasta
  163. efloden 49843 0.1 0.8 1182432 1168136 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  164. efloden 8998 0.0 0.0 4324 644 ? S 11:27 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497498433794.pl one seq aln 2PARAM
  165. efloden 9367 0.0 0.0 20892 3344 ? S 11:27 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497498433794.pl one seq aln 2PARAM
  166. efloden 9613 0.0 0.0 4324 640 ? S 11:27 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  167. efloden 9700 0.0 0.0 58904 18636 ? S 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  168. efloden 11879 0.1 0.0 137372 28136 ? Sl 11:27 0:01 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/backbone/backbone3FaxD0.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/
  169. efloden 14677 0.0 0.0 194224 16584 ? Sl 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/backbone/backbone3FaxD0.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/
  170. efloden 15952 0.0 0.0 63248 18660 ? S 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/backbone/backbone3FaxD0.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/
  171. efloden 31522 6.1 0.0 11192 4748 ? R 11:34 0:08 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/pastajob/temphM634B/step0/mincluster/tempfasttree5JwpP5/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/pastajob/temphM634B/step0/mincluster/tempfasttree5JwpP5/log /scratch/29787929.1.long-sl7/sepp/seq.aln.oGcpZG/pastaout/pastajob/temphM634B/step0/mincluster/tempfasttree5JwpP5/input.fasta
  172. efloden 50126 0.1 0.8 1181080 1166772 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  173. efloden 59839 0.0 0.0 4324 640 ? S 11:27 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497501263794.pl one seq aln 2PARAM
  174. efloden 60162 0.0 0.0 20892 3348 ? S 11:27 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497501263794.pl one seq aln 2PARAM
  175. efloden 60378 0.0 0.0 4324 636 ? S 11:27 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  176. efloden 60464 0.0 0.0 58904 18676 ? S 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  177. efloden 62731 0.3 0.0 149604 40520 ? Sl 11:27 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/backbone/backbone5TVpzk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/
  178. efloden 65085 0.0 0.0 194216 16576 ? Sl 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/backbone/backbone5TVpzk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/
  179. efloden 1211 0.0 0.0 64536 19716 ? S 11:27 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/backbone/backbone5TVpzk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/
  180. efloden 49667 0.0 0.0 4324 656 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/pastajob/tempgxPu5Q/step1/mincluster/r1/d2/tempmafftZSKttY/input.fasta
  181. efloden 49730 0.0 0.0 4716 1080 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/pastajob/tempgxPu5Q/step1/mincluster/r1/d2/tempmafftZSKttY/input.fasta
  182. efloden 51471 0.0 0.0 4716 740 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.CBlirN/pastaout/pastajob/tempgxPu5Q/step1/mincluster/r1/d2/tempmafftZSKttY/input.fasta
  183. efloden 25414 6.2 0.0 142272 20412 ? Sl 11:35 0:01 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/dvtditr -s 0.0 -C 1 -t 0 -F -l 2.7 -z 50 -b 62 -f -1.53 -Q 100.0 -h -0.123 -I 16 -X -p BAATARI2
  184. efloden 50388 0.0 0.8 1180456 1166268 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  185. efloden 22820 0.0 0.0 4324 640 ? S 11:34 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497503883669.pl one seq aln 2PARAM
  186. efloden 23093 0.0 0.0 20892 3348 ? S 11:34 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497503883669.pl one seq aln 2PARAM
  187. efloden 23271 0.0 0.0 4324 640 ? S 11:34 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  188. efloden 23378 0.1 0.0 58904 18596 ? S 11:34 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  189. efloden 25306 0.3 0.0 130876 21144 ? Sl 11:34 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/backbone/backboneRxCfUi.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/
  190. efloden 27669 0.0 0.0 194228 16704 ? Sl 11:34 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/backbone/backboneRxCfUi.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/
  191. efloden 28658 0.0 0.0 62820 18196 ? S 11:34 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/backbone/backboneRxCfUi.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/
  192. efloden 5516 6.0 0.0 10312 3904 ? R 11:35 0:04 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -log /scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/pastajob/tempINvOXK/init_tree/tempfasttreeekL2s9/log /scratch/29787929.1.long-sl7/sepp/seq.aln.7hY6EV/pastaout/pastajob/tempINvOXK/init_tree/tempfasttreeekL2s9/input.fasta
  193. efloden 50661 0.0 0.8 1180056 1165840 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  194. efloden 42864 0.0 0.8 1180056 1165184 ? R 11:36 0:00 | | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  195. efloden 50889 0.0 0.8 1179564 1165380 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  196. efloden 59801 0.0 0.0 4324 644 ? S 10:57 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497508893669.pl one seq aln 2PARAM
  197. efloden 60187 0.0 0.0 20892 3348 ? S 10:57 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497508893669.pl one seq aln 2PARAM
  198. efloden 60590 0.0 0.0 4324 640 ? S 10:57 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  199. efloden 60720 0.0 0.0 58904 18680 ? S 10:57 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  200. efloden 63895 0.1 0.0 154844 46832 ? Sl 10:57 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/backbone/backbone1nvidn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/
  201. efloden 1301 0.0 0.0 194216 16592 ? Sl 10:57 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/backbone/backbone1nvidn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/
  202. efloden 3305 0.0 0.0 66760 21924 ? S 10:57 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/backbone/backbone1nvidn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/
  203. efloden 57845 6.1 0.0 21932 15476 ? R 11:27 0:34 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/pastajob/tempYBzicB/step0/mincluster/tempfasttree_oPzah/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/pastajob/tempYBzicB/step0/mincluster/tempfasttree_oPzah/log /scratch/29787929.1.long-sl7/sepp/seq.aln.HGFv5N/pastaout/pastajob/tempYBzicB/step0/mincluster/tempfasttree_oPzah/input.fasta
  204. efloden 51252 0.0 0.8 1180816 1166576 ? S 10:40 0:00 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  205. efloden 53250 0.0 0.0 4324 644 ? S 10:40 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497512523669.pl one seq aln 2PARAM
  206. efloden 53798 0.0 0.0 20892 3348 ? S 10:40 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497512523669.pl one seq aln 2PARAM
  207. efloden 54309 0.0 0.0 4324 640 ? S 10:40 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  208. efloden 54511 0.0 0.0 58892 18676 ? S 10:40 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  209. efloden 60068 0.1 0.0 163624 54404 ? Sl 10:41 0:03 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/backbone/backboneKQVoZu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/
  210. efloden 1629 0.0 0.0 194216 16568 ? Sl 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/backbone/backboneKQVoZu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/
  211. efloden 4682 0.0 0.0 64552 19820 ? S 10:41 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/backbone/backboneKQVoZu.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/
  212. efloden 42564 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/pastajob/tempP2GZWM/step2/mincluster/r2/d1/tempmafftddcu6B/input.fasta
  213. efloden 42619 0.0 0.0 4324 644 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/pastajob/tempP2GZWM/step2/mincluster/r2/d1/tempmafftddcu6B/input.fasta
  214. efloden 42860 0.0 0.0 4324 112 ? R 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.32bf7I/pastaout/pastajob/tempP2GZWM/step2/mincluster/r2/d1/tempmafftddcu6B/input.fasta
  215. efloden 51597 0.0 0.8 1179712 1165528 ? S 10:40 0:01 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  216. efloden 52232 0.0 0.0 4324 644 ? S 10:51 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497515973794.pl one seq aln 2PARAM
  217. efloden 52579 0.0 0.0 20892 3348 ? S 10:51 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497515973794.pl one seq aln 2PARAM
  218. efloden 52916 0.0 0.0 4324 636 ? S 10:51 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  219. efloden 53046 0.0 0.0 58892 18684 ? S 10:51 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  220. efloden 56402 0.1 0.0 169116 61316 ? Sl 10:51 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/backbone/backbone3LM3Dy.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/
  221. efloden 59785 0.0 0.0 194216 16584 ? Sl 10:51 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/backbone/backbone3LM3Dy.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/
  222. efloden 62247 0.0 0.0 66520 21692 ? S 10:51 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/backbone/backbone3LM3Dy.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/
  223. efloden 54337 0.0 0.0 4324 652 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/pastajob/tempqOjKQZ/step1/mincluster/r3/d2/tempmafftKRHIOV/input.fasta
  224. efloden 54379 0.0 0.0 4716 1084 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/pastajob/tempqOjKQZ/step1/mincluster/r3/d2/tempmafftKRHIOV/input.fasta
  225. efloden 56036 0.0 0.0 4716 744 ? S 11:34 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln._WRJGm/pastaout/pastajob/tempqOjKQZ/step1/mincluster/r3/d2/tempmafftKRHIOV/input.fasta
  226. efloden 25970 6.0 0.0 143652 23888 ? Sl 11:35 0:01 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/dvtditr -s 0.0 -C 1 -t 0 -F -l 2.7 -z 50 -b 62 -f -1.53 -Q 100.0 -h -0.123 -I 16 -X -p BAATARI2
  227. efloden 51990 0.1 0.8 1183372 1169172 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  228. efloden 24481 0.0 0.0 4324 644 ? S 11:21 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497519903669.pl one seq aln 2PARAM
  229. efloden 24818 0.0 0.0 20892 3344 ? S 11:21 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497519903669.pl one seq aln 2PARAM
  230. efloden 25080 0.0 0.0 4324 636 ? S 11:21 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  231. efloden 25202 0.0 0.0 58908 18680 ? S 11:21 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  232. efloden 27942 0.3 0.0 158412 49932 ? Sl 11:21 0:02 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/backbone/backbonexDgx_O.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/
  233. efloden 30872 0.0 0.0 194228 16584 ? Sl 11:21 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/backbone/backbonexDgx_O.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/
  234. efloden 32333 0.0 0.0 64192 19568 ? S 11:21 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/backbone/backbonexDgx_O.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/
  235. efloden 37010 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/pastajob/tempw01Qvj/step2/mincluster/r0/d2/tempmaffttXYjb9/input.fasta
  236. efloden 37059 0.0 0.0 4716 1080 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/pastajob/tempw01Qvj/step2/mincluster/r0/d2/tempmaffttXYjb9/input.fasta
  237. efloden 38648 0.0 0.0 4716 700 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.aZ0Sw8/pastaout/pastajob/tempw01Qvj/step2/mincluster/r0/d2/tempmaffttXYjb9/input.fasta
  238. efloden 38798 6.4 0.0 113196 7012 ? Sl 11:36 0:00 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign -u 0.0 -l 2.7 -C 1 -b 62 -g -0.100 -f -2.00 -Q 100.0 -h 0.1 -L
  239. efloden 52324 0.0 0.8 1180200 1166016 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  240. efloden 12382 0.0 0.0 4324 644 ? S 11:11 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497523243669.pl one seq aln 2PARAM
  241. efloden 12739 0.0 0.0 20892 3348 ? S 11:11 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497523243669.pl one seq aln 2PARAM
  242. efloden 13076 0.0 0.0 4324 640 ? S 11:11 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  243. efloden 13180 0.0 0.0 58908 18676 ? S 11:11 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  244. efloden 16610 0.2 0.0 172164 64096 ? Sl 11:11 0:04 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/backbone/backboneinHpSg.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/
  245. efloden 19585 0.0 0.0 194216 16708 ? Sl 11:11 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/backbone/backboneinHpSg.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/
  246. efloden 21647 0.0 0.0 65212 20552 ? S 11:11 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/backbone/backboneinHpSg.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/
  247. efloden 30732 6.0 0.0 8864 2216 ? R 11:36 0:01 | | | \_ /pasta-code/pasta/bin/fasttree -quiet -wag -gamma -fastest -intree /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/pastajob/tempphk0uQ/step2/mincluster/tempfasttreeP0Gzpq/start.tre -log /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/pastajob/tempphk0uQ/step2/mincluster/tempfasttreeP0Gzpq/log /scratch/29787929.1.long-sl7/sepp/seq.aln.BWNrmp/pastaout/pastajob/tempphk0uQ/step2/mincluster/tempfasttreeP0Gzpq/input.fasta
  248. efloden 52765 0.1 0.8 1180740 1166428 ? S 10:40 0:03 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  249. efloden 33721 0.1 0.0 4324 644 ? S 11:36 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497527653669.pl one seq aln 2PARAM
  250. efloden 33916 0.0 0.0 20892 3344 ? S 11:36 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497527653669.pl one seq aln 2PARAM
  251. efloden 34048 0.0 0.0 4324 636 ? S 11:36 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  252. efloden 34115 1.3 0.0 58904 18528 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  253. efloden 36004 2.5 0.0 129784 19948 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/backbone/backbonemmHRrb.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/
  254. efloden 38215 0.1 0.0 194228 16728 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/backbone/backbonemmHRrb.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/
  255. efloden 38652 0.0 0.0 61892 17176 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/backbone/backbonemmHRrb.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/
  256. efloden 41228 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/pastajob/temppUyuaz/step0/mincluster/r0/d1/tempmafftEreYuh/input.fasta
  257. efloden 41314 0.0 0.0 4716 1076 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/pastajob/temppUyuaz/step0/mincluster/r0/d1/tempmafftEreYuh/input.fasta
  258. efloden 42540 0.0 0.0 4716 736 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/pastajob/temppUyuaz/step0/mincluster/r0/d1/tempmafftEreYuh/input.fasta
  259. efloden 42875 0.0 0.0 4716 508 ? R 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.wv7sJ6/pastaout/pastajob/temppUyuaz/step0/mincluster/r0/d1/tempmafftEreYuh/input.fasta
  260. efloden 53070 0.1 0.8 1181492 1167284 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  261. efloden 11496 0.0 0.0 4324 644 ? S 11:35 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497530703669.pl one seq aln 2PARAM
  262. efloden 11757 0.0 0.0 20892 3348 ? S 11:35 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497530703669.pl one seq aln 2PARAM
  263. efloden 11969 0.0 0.0 4324 640 ? S 11:35 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  264. efloden 12059 0.3 0.0 58904 18524 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  265. efloden 14156 0.6 0.0 129936 20368 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/backbone/backboneTfQV30.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/
  266. efloden 16188 0.0 0.0 194228 16720 ? Sl 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/backbone/backboneTfQV30.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/
  267. efloden 16699 0.0 0.0 61892 17188 ? S 11:35 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/backbone/backboneTfQV30.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/
  268. efloden 42372 5.0 0.0 1777348 20924 ? Sl 11:36 0:00 | | | \_ java -Xmx1024m -jar /pasta-code/pasta/bin/opal.jar --in /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/pastajob/tempY46B1m/step2/mincluster/pw/tempopalcrZD7k/1_U2X.fasta --in2 /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/pastajob/tempY46B1m/step2/mincluster/pw/tempopalcrZD7k/2_U2X.fasta --out /scratch/29787929.1.long-sl7/sepp/seq.aln.Xjpgn6/pastaout/pastajob/tempY46B1m/step2/mincluster/pw/tempopalcrZD7k/out_rep.fasta --align_method profile
  269. efloden 53474 0.1 0.8 1181132 1166948 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  270. efloden 41131 0.0 0.0 4324 640 ? S 11:28 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497534743669.pl one seq aln 2PARAM
  271. efloden 41249 0.0 0.0 20892 3348 ? S 11:28 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497534743669.pl one seq aln 2PARAM
  272. efloden 41355 0.0 0.0 4324 636 ? S 11:28 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  273. efloden 41408 0.0 0.0 58892 18676 ? S 11:28 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  274. efloden 42876 0.2 0.0 141348 31852 ? Sl 11:28 0:01 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/backbone/backboneL6O3tk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/
  275. efloden 44357 0.0 0.0 194228 16564 ? Sl 11:28 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/backbone/backboneL6O3tk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/
  276. efloden 45198 0.0 0.0 64052 19420 ? S 11:28 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/backbone/backboneL6O3tk.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/
  277. efloden 6770 0.0 0.0 4324 656 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/pastajob/temp6d6th5/step0/mincluster/r1/d1/tempmafftZt_zLE/input.fasta
  278. efloden 6833 0.0 0.0 4716 1080 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/pastajob/temp6d6th5/step0/mincluster/r1/d1/tempmafftZt_zLE/input.fasta
  279. efloden 8265 0.0 0.0 4716 740 ? S 11:35 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.goZGuO/pastaout/pastajob/temp6d6th5/step0/mincluster/r1/d1/tempmafftZt_zLE/input.fasta
  280. efloden 41441 6.0 0.0 117564 8132 ? Sl 11:36 0:00 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/tbfast -s 0.0 -O -C 1 -b 62 -f -1.53 -Q 100.0 -h -0.123 -F -l 2.7 -X
  281. efloden 53999 0.1 0.8 1181460 1167260 ? S 10:40 0:05 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  282. efloden 30804 0.0 0.0 4324 644 ? S 11:36 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497539993669.pl one seq aln 2PARAM
  283. efloden 31054 0.0 0.0 20892 3348 ? S 11:36 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497539993669.pl one seq aln 2PARAM
  284. efloden 31198 0.0 0.0 4324 640 ? S 11:36 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  285. efloden 31287 1.0 0.0 58904 18528 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  286. efloden 33291 1.7 0.0 129828 20084 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/backbone/backbonenJ5W69.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/
  287. efloden 35151 0.0 0.0 194228 16720 ? Sl 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/backbone/backbonenJ5W69.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/
  288. efloden 35573 0.0 0.0 61892 17172 ? S 11:36 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/backbone/backbonenJ5W69.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/
  289. efloden 42392 0.0 0.0 4324 656 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/pastajob/tempMcssPl/step1/mincluster/r0/d1/tempmafftbjWN7v/input.fasta
  290. efloden 42432 0.0 0.0 4324 672 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/pastajob/tempMcssPl/step1/mincluster/r0/d1/tempmafftbjWN7v/input.fasta
  291. efloden 42892 0.0 0.0 4324 112 ? R 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.ibbouo/pastaout/pastajob/tempMcssPl/step1/mincluster/r0/d1/tempmafftbjWN7v/input.fasta
  292. efloden 54452 0.1 0.8 1181080 1166896 ? S 10:40 0:04 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  293. efloden 50287 0.0 0.0 4324 644 ? S 11:19 0:00 | | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497544523669.pl one seq aln 2PARAM
  294. efloden 50553 0.0 0.0 20892 3348 ? S 11:19 0:00 | | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497544523669.pl one seq aln 2PARAM
  295. efloden 50873 0.0 0.0 4324 640 ? S 11:19 0:00 | | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  296. efloden 50999 0.0 0.0 58892 18680 ? S 11:19 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  297. efloden 54272 0.3 0.0 169376 61056 ? Sl 11:19 0:03 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/backbone/backbone1y_IAM.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/
  298. efloden 57403 0.0 0.0 194228 16580 ? Sl 11:19 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/backbone/backbone1y_IAM.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/
  299. efloden 59324 0.0 0.0 66276 21564 ? S 11:19 0:00 | | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/backbone/backbone1y_IAM.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/
  300. efloden 36318 0.0 0.0 4324 652 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/pastajob/tempMeHMFS/step1/mincluster/r0/d2/tempmafft17o6K6/input.fasta
  301. efloden 36410 0.0 0.0 4716 1076 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/pastajob/tempMeHMFS/step1/mincluster/r0/d2/tempmafft17o6K6/input.fasta
  302. efloden 37841 0.0 0.0 4716 696 ? S 11:36 0:00 | | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.9YSslA/pastaout/pastajob/tempMeHMFS/step1/mincluster/r0/d2/tempmafft17o6K6/input.fasta
  303. efloden 38011 6.0 0.0 113196 6768 ? Sl 11:36 0:00 | | | \_ /pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign -u 0.0 -l 2.7 -C 1 -b 62 -g -0.100 -f -2.00 -Q 100.0 -h 0.1 -L
  304. efloden 54952 0.0 0.8 1180200 1166016 ? S 10:40 0:02 | | \_ t_coffee -dpa -dpa_method upp_msa -dpa_tree PF02771.CLUSTALO.dnd -seq PF02771.fa -dpa_nseq 1000 -outfile PF02771.dpa_1000.UPP.with.CLUSTALO.tree.aln -n_core=1
  305. efloden 5495 0.0 0.0 4324 644 ? S 11:12 0:00 | | \_ sh -c /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497549523669.pl one seq aln 2PARAM
  306. efloden 5949 0.0 0.0 20892 3344 ? S 11:12 0:00 | | \_ perl /scratch/29787929.1.long-sl7/.tcoffee/tmp/tco/tcouydoqe5940203/73497549523669.pl one seq aln 2PARAM
  307. efloden 6359 0.0 0.0 4324 640 ? S 11:12 0:00 | | \_ sh -c fbname=$(basename `ls *.seq` .seq); run_upp.py -s ${fbname}.seq -m amino --cpu 1 -d outdir -o ${fbname}.aln; mv outdir/${fbname}.aln_alignment.fasta ${fbname}.aln;
  308. efloden 6544 0.0 0.0 58892 18684 ? S 11:12 0:00 | | \_ /usr/bin/python /usr/local/bin/run_upp.py -s seq.seq -m amino --cpu 1 -d outdir -o seq.aln
  309. efloden 10157 0.2 0.0 169788 61668 ? Sl 11:12 0:03 | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/backbone/backbone4AKkSn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/
  310. efloden 13499 0.0 0.0 194228 16560 ? Sl 11:12 0:00 | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/backbone/backbone4AKkSn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/
  311. efloden 15923 0.0 0.0 66260 21472 ? S 11:12 0:00 | | \_ /usr/bin/python /usr/local/bin/run_pasta.py --num-cpus=1 -i /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/backbone/backbone4AKkSn.fas --datatype=protein --temporaries=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/ -j pastajob --output-directory=/scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/
  312. efloden 29481 0.0 0.0 4324 656 ? S 11:36 0:00 | | \_ /bin/sh /pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/pastajob/tempFBQw6B/step1/mincluster/r3/d2/tempmaffttjvA46/input.fasta
  313. efloden 29562 0.0 0.0 4716 1080 ? S 11:36 0:00 | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/pastajob/tempFBQw6B/step1/mincluster/r3/d2/tempmaffttjvA46/input.fasta
  314. efloden 31069 0.0 0.0 4716 700 ? S 11:36 0:00 | | \_ /bin/sh /pasta-code/pasta/bin/mafftdir/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /scratch/29787929.1.long-sl7/sepp/seq.aln.pSYEtg/pastaout/pastajob/tempFBQw6B/step1/mincluster/r3/d2/tempmaffttjvA46/input.fasta
  315. efloden 31201 6.0 0.0 113192 6592 ? Sl 11:36 0:01 | | \_ /pasta-code/pasta/bin/mafftdir/libexec/pairlocalalign -u 0.0 -l 2.7 -C 1 -b 62 -g -0.100 -f -2.00 -Q 100.0 -h 0.1 -L
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