Running realignment error

[ramoserica]

Hello,

I have started an alignment from a previous attempt and I've got the following error in cactus.log (attached file). Does anyone know how to solve it?

"Continuing existing alignment. Use --overwrite or erase the working directory to force restart from scratch.

2015-11-17 17:56:25.822383: Beginning Progressive Cactus Alignment

Got message from job at time: 1447790240.1 : Running blast using the trimming strategy Got message from job at time: 1447790240.11 : Ingroup sequences: ['/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8B RJw/renamedInputs/simPscalare.fa_4', '/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8BRJw/renamedInputs/simSpecie1. fa_3'] Got message from job at time: 1447790240.11 : Outgroup sequences: ['/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8 BRJw/renamedInputs/simAocellatus.fa_2', '/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8BRJw/renamedInputs/simSpecie2 oleri.fa_1', '/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8BRJw/renamedInputs/simOniloticus.fa_0'] Got message from job at time: 1447790256.36 : Blasting ingroups vs outgroups to file /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/job s/gTD5/tmp_IgKXP8BRJw/tmp_Lgq5Jdn5d7unconvertedAlignments Got message from job at time: 1448205427.66 : Coverage on simSpecie3.fa_4 from outgroup #1, simSpecie4.fa_2: 72.204245448% (current ingroup length 906169248, untrim med length 906169248). Outgroup trimmed to 985032453 bp from 1030552047 Got message from job at time: 1448205427.66 : Coverage on simSpecie1.fa_3 from outgroup #1, simSpecie4.fa_2: 69.4662393021% (current ingroup length 930627399, untrim med length 930627399). Outgroup trimmed to 985032453 bp from 1030552047 Got message from job at time: 1448205427.66 : Cumulative coverage of 1 outgroups on ingroup simSpecie3.fa_4: 72.204245448 Got message from job at time: 1448205427.66 : Cumulative coverage of 1 outgroups on ingroup simSpecie1.fa_3: 69.4662393021 Got message from job at time: 1448252594.62 : Coverage on simSpecie3.fa_4 from outgroup #2, simSpecie2.fa_1: 41.2475396329% (current ingroup length 313767202, untri mmed length 906169248). Outgroup trimmed to 940601391 bp from 1078160618 Got message from job at time: 1448252594.62 : Coverage on simSpecie1.fa_3 from outgroup #2, simSpecie2.fa_1: 38.6040527016% (current ingroup length 332156551, untrim med length 930627399). Outgroup trimmed to 940601391 bp from 1078160618 Got message from job at time: 1448252594.62 : Cumulative coverage of 2 outgroups on ingroup simSpecie3.fa_4: 76.5728675445 Got message from job at time: 1448252594.62 : Cumulative coverage of 2 outgroups on ingroup simSpecie1.fa_3: 73.6743670707 Got message from job at time: 1448282454.18 : Coverage on simSpecie3.fa_4 from outgroup #3, simSpecie5.fa_0: 27.6055235586% (current ingroup length 276640571, untri mmed length 906169248). Outgroup trimmed to 783602633 bp from 927679487 Got message from job at time: 1448282454.18 : Coverage on simSpecie1.fa_3 from outgroup #3, simSpecie5.fa_0: 26.1683206045% (current ingroup length 293885898, untrim med length 930627399). Outgroup trimmed to 783602633 bp from 927679487 Got message from job at time: 1448282454.18 : Cumulative coverage of 3 outgroups on ingroup simSpecie3.fa_4: 76.9479374343 Got message from job at time: 1448282454.18 : Cumulative coverage of 3 outgroups on ingroup simSpecie1.fa_3: 74.0329706325 Got message from job at time: 1448282639.95 : Blocking on ktserver <kyoto_tycoon database_dir="/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/progressiveAlignment/Anc3/Anc3/Anc3_DB" database_name="Anc3.kch" in_memory="1" port="1981" snapshot="0" />

with killPath /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8BRJw/tmp_oh9aEV4Zpk_kill.txt Got message from job at time: 1448288013.63 : Converted headers of cigar file /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/gTD5/tmp_IgKXP8BRJw/tmp_Lgq5Jdn5d7unconvertedAlignments to internal names, new file /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/gTD1/tmp_7rROFWws6v/tmp_1CvRjl1U3h Got message from job at time: 1448288013.63 : Starting caf phase target with index 0 at 1448288013.57 seconds (recursing = 1) The job seems to have left a log file, indicating failure: /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/job Reporting file: /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: sort: write failed: standard output: No space left on device log.txt: sort: write error log.txt: Encountered unix sort error when sorting cigar alignments in file: /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/gTD1/tmp_7rROFWws6v/tmp_1CvRjl1U3h log.txt:
log.txt: Traceback (most recent call last): log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/cactus/pipeline/cactus_workflow.py", line 538, in run log.txt: self.runCactusCafInWorkflow(alignmentFile=self.phaseNode.attrib["alignments"]) log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/cactus/pipeline/cactus_workflow.py", line 504, in runCactusCafInWorkflow log.txt: realignArguments=self.getOptionalPhaseAttrib("realignArguments")) log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/cactus/shared/common.py", line 239, in runCactusCaf log.txt: masterMessages = popenCatch(command, stdinString=flowerNames) log.txt: File "/mnt/erica/progressiveCactus_copy/submodules/sonLib/bioio.py", line 211, in popenCatch log.txt: raise RuntimeError("Command: %s with stdin string '%s' exited with non-zero status %i" % (command, stdinString, sts)) log.txt: RuntimeError: Command: cactus_caf --cactusDisk '<st_kv_database_conf type="kyoto_tycoon"> log.txt: <kyoto_tycoon database_dir="/mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/progressiveAlignment/Anc3/Anc3/Anc3_DB" database_name="Anc3.kch" host="thomas" in_memory="1" port="1981" snapshot="0" /> log.txt: </st_kv_database_conf> log.txt: ' --logLevel CRITICAL --alignments /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/gTD1/tmp_7rROFWws6v/tmp_1CvRjl1U3h --annealingRounds '128' --deannealingRounds '2 8' --trim '0 0' --minimumTreeCoverage 0.0 --blockTrim 5 --minimumDegree 2 --minimumIngroupDegree 2 --minimumOutgroupDegree 0 --singleCopyOutgroup --lastzArguments '--step=1 --ambiguous=iupac,100,100 --ydrop=3000 --identity=25.0' --minimumSequenceLengthForBlast 30 --maxAdjacencyComponentSizeRatio 50.0 --minLengthForChromosome 1000000 --proportionOfUnalignedBasesForNewChromosome 0.8 --maximumMedianSequenceLengthBetweenLinkedEnds 1000 --realign --realignArguments '--gapGamma 0.9 --diagonalExpansion 4 --splitMatrixBiggerThanThis 10 --constraintDiagonalTrim 0 --alignAmbiguityCharacters --splitIndelsLongerThanThis 99' with stdin string '1 0' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host thomas log.txt: Due to failure we are reducing the remaining retry count of job /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/job to 0 log.txt: We have set the default memory of the failed job to 137438953472 bytes Job: /mnt/erica/assemblies_finalversion_newtest/comparative_cactus/test2_tmp/jobTree/jobs/t1/job is completely failed"