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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Bad fasta character #50

Open Tetrajf opened 8 years ago

Tetrajf commented 8 years ago

Dear Cactus team.

Sorry for the dumb error but I'm stuck. I'm getting errors for bad fasta characters. I have of course removed any non-AGCT characters as well any lower case symbols. I will email a log. Regards J

glennhickey commented 8 years ago

Pretty weird that even the example doesn't run. Does it work with --database tokyo_cabinet? ie:

rm -rf work ; bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal --databse tokyo_cabinet

On Tue, Nov 10, 2015 at 10:53 AM, Tetrajf notifications@github.com wrote:

Dear Cactus team.

Sorry for the dumb error but I'm stuck. I'm getting errors for bad fasta characters. I have of course removed any non-AGCT characters as well any lower case symbols. I will email a log. Regards J

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/50.

Tetrajf commented 8 years ago

Ok I'll give that a try. Thanks.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: Glenn Hickey notifications@github.com Date:10/11/2015 8:20 PM (GMT+02:00) To: glennhickey/progressiveCactus progressiveCactus@noreply.github.com Cc: Tetrajf j_featherston@yahoo.com Subject: Re: [progressiveCactus] Bad fasta character (#50)

Pretty weird that even the example doesn't run. Does it work with -database tokyo_cabinet? ie: rm -rf work ; bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal -databse tokyo_cabinet On Tue, Nov 10, 2015 at 10:53 AM, Tetrajf notifications@github.com wrote: > Dear Cactus team. > > Sorry for the dumb error but I'm stuck. I'm getting errors for bad fasta > characters. I have of course removed any non-AGCT characters as well any > lower case symbols. > I will email a log. > Regards > J > > — > Reply to this email directly or view it on GitHub > https://github.com/glennhickey/progressiveCactus/issues/50. > —Reply to this email directly or view it on GitHub.

glennhickey commented 8 years ago

(Pasting some relevant stuff from the files you sent me here so other developers can see them. I'm stumped) blanchette example log

Got message from job at time: 1447171876.38 : Starting bar phase target with index 0 at 1447171876.1 seconds (recursing = 1) The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Read only 0 bytes of string of length 9094 when caching substrings from DB log.txt: log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 188 9203950263461676184 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 29 16 16 16 16 4 1 2584 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 4 3154 13 13 13 13 13 13 13 13 13 13 13 13 13 13 4 200 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 29 4 1320 16 16 16 16 16 16 16 16 16 16 16 16 16 16 118 16 16 16 16 16 16 16 16 16 16 16 16 16 4 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Read only 0 bytes of string of length 4259 when caching substrings from DB log.txt: log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 6 9203950263461686172 16 16 13 13 4 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job is completely failed

On Tue, Nov 10, 2015 at 1:55 PM, Tetrajf notifications@github.com wrote:

Ok I'll give that a try. Thanks.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: Glenn Hickey notifications@github.com Date:10/11/2015 8:20 PM (GMT+02:00) To: glennhickey/progressiveCactus progressiveCactus@noreply.github.com Cc: Tetrajf j_featherston@yahoo.com Subject: Re: [progressiveCactus] Bad fasta character (#50)

Pretty weird that even the example doesn't run. Does it work with -database tokyo_cabinet? ie: rm -rf work ; bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal -databse tokyo_cabinet On Tue, Nov 10, 2015 at 10:53 AM, Tetrajf notifications@github.com wrote:

Dear Cactus team. > > Sorry for the dumb error but I'm stuck. I'm getting errors for bad fasta > characters. I have of course removed any non-AGCT characters as well any > lower case symbols. > I will email a log. > Regards > J > > — > Reply to this email directly or view it on GitHub > < https://github.com/glennhickey/progressiveCactus/issues/50>. > —Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/50#issuecomment-155530471 .

glennhickey commented 8 years ago

(and original log. unlike blanchette log, where bar is still dying, this one also shows a lastz error complaining about piped in fasta)

Got message from job at time: 1447087275.18 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusBarWrapperLarge'> and stats flower name: 4308255993533285646 total bases: 3380315 total-ends: 700 total-caps: 1768 max-end-degree: 21 max-adjacency-length: 47394 total-blocks: 0 total-groups: 1 total-edges: 715 total-free-ends: 138 total-attached-ends: 562 total-chains: 0 total-link groups: 0 The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: FAILURE: bad fasta character in /tmp/stTmp32565_0, >a (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using --ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz --hspthresh=800 --chain --strand=plus --gapped --format=cigar --ambiguous=iupac,100,100 /tmp/stTmp32565_0 /tmp/stTmp32565_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/bin/work/progressiveAlignment/859/859/859_DB" database_name="859.kch" host="10.128.1.4" in_memory="1" port="1980" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 2008 631770585227063177 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: FAILURE: bad fasta character in /tmp/stTmp32568_0, >a (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using --ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command echo '>b log.txt: GGCGCGGACGTGGGGGGCCCGGCAGCAGACGCGCAGGACGGCGGCTCCGGCGGCAACGGCACTGACGTGAATGCCTATATCCGGGGGGACTACTCGCTAATGTCGCCCTCGGGCCTGCAGCCCCCCCACTCGCCTTCAGCTCCTTCCTCACAACAACTACCAGGTGCCTCCGGGCATCGGAACACCCCCCAGCAGCAGCCGCAGCCGCAGCAGCAGCGAACCCAGCAGCCACATCCACAACCGGAGCAGGGAGCTAGTCAGCAGCCCCAGCCACACAGGCAGCATCGCCTGTGGGCTTGTAATAACAACAACAATAACAACAACCAGCAGCAGCAATACAGCCATCAAAACCAGCAGCTGGTGTCCACGGGGCATCAGGAGATGCGGAGCTCAGATGACCGTAAGGAAGCTACGGGATCGGGCTCgcagctgcagcagccgcaccaccatcgccatcaccatcaccatcatcataatcaccatcatcatcgccacccccagcatgcga log.txt: ' | cactus_lastz --hspthresh=800 --chain --strand=plus --gapped --format=cigar --ambiguous=iupac,100,100 /tmp/stTmp32568_0 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/bin/work/progressiveAlignment/859/859/859_DB" database_name="859.kch" host="10.128.1.4" in_memory="1" port="1980" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 2433 631770585227075125 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 496381121429221955 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: FAILURE: bad fasta character in /tmp/stTmp32570_1, >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using --ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz --hspthresh=800 --chain --strand=plus --gapped --format=cigar --ambiguous=iupac,100,100 /tmp/stTmp32570_0 /tmp/stTmp32570_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/bin/work/progressiveAlignment/859/859/859_DB" database_name="859.kch" host="10.128.1.4" in_memory="1" port="1980" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 2594 2246451789127745558 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 505529058172318210 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: FAILURE: bad fasta character in (stdin), >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using --ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command echo '>b log.txt: GGCGGCGTTGACGGGGGTAGGTTGACCGGGGTGACGGGAGTGGGCATGCGCGCATGGGCCCGGATGCTGTATGGCGGGGCCGGTGCACCTGGGTGAGCCTGCCTGATGTATGCGCGGATGCGGATGGGCGACCTGCCACAGCGCCCGGCAGGGGCAAGAGCCACATTGCCGGCATCGCGCGCCACAGTTACTGCAGCTAGCATGAGCTGCCTAGCGTGGCTCTCGGTGTCCGCATGCTCCCATCCTCGTCACCGTTTCCCTGACGCCTACACTTCAGGTCGGGCTAGCGCTGGCGGTAGCTCGCAAGGCCGCGCCGCCCGACTGCATCCGCGCGGCGCTGGACCCGGCCCGGCCGCACATCACGCCACCCACCGCGCCGCCCACTGGCCTGATGATGGTGAGCGCTGGGGCCGCCGCCGCGGA>CACTGAGGACACATGCCACACTGCCGTGTCGTTGTGCCACCAAGTGCACCACTGGGGACACCCCCGCAGCGCCCCGACCTGTAACTGGATGCTTATCTTACTGGTGCAGGAATGGAGCAGGGTAAGGGCGTGGGGAAGGCGCAGGGTGGCGCGGTCCCGATAGTGTGCAGCGTACGATATCCCCGTCTTACTGGTCTTAT log.txt: ' | cactus_lastz --hspthresh=800 --chain --strand=plus --gapped --format=cigar --ambiguous=iupac,100,100 /tmp/stTmp32569_3 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/bin/work/progressiveAlignment/859/859/859_DB" database_name="859.kch" host="10.128.1.4" in_memory="1" port="1980" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 1231 1128151706656311672 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 1118300082471411968 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t4/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t4/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: FAILURE: bad fasta character in /tmp/stTmp32598_1, >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using --ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz --hspthresh=800 --chain --strand=plus --gapped --format=cigar --ambiguous=iupac,100,100 /tmp/stTmp32598_0 /tmp/stTmp32598_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/bin/work/progressiveAlignment/859/859/859_DB" database_name="859.kch" host="10.128.1.4" in_memory="1" port="1980" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 769 3049640635171594237 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 56154257853759091 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1

On Tue, Nov 10, 2015 at 4:19 PM, Glenn Hickey glenn.hickey@gmail.com wrote:

(Pasting some relevant stuff from the files you sent me here so other developers can see them. I'm stumped) blanchette example log

Got message from job at time: 1447171876.38 : Starting bar phase target with index 0 at 1447171876.1 seconds (recursing = 1) The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Read only 0 bytes of string of length 9094 when caching substrings from DB log.txt: log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 188 9203950263461676184 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 29 16 16 16 16 4 1 2584 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 4 3154 13 13 13 13 13 13 13 13 13 13 13 13 13 13 4 200 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 29 4 1320 16 16 16 16 16 16 16 16 16 16 16 16 16 16 118 16 16 16 16 16 16 16 16 16 16 16 16 16 4 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Read only 0 bytes of string of length 4259 when caching substrings from DB log.txt: log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar --cactusDisk ' log.txt: <kyoto_tycoon database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" snapshot="0" /> log.txt: log.txt: ' --logLevel CRITICAL --spanningTrees 5 --maximumLength 100000 --gapGamma 0.2 --splitMatrixBiggerThanThis 3000 --anchorMatrixBiggerThanThis 500 --repeatMaskMatrixBiggerThanThis 500 --constraintDiagonalTrim 14 --minimumDegree 2 --minimumIngroupDegree 0 --minimumOutgroupDegree 0 --alignAmbiguityCharacters --pruneOutStubAlignments --diagonalExpansion 20 --maximumNumberOfSequencesBeforeSwitchingToFast 10 --largeEndSize 5000 with stdin string ' 6 9203950263461686172 16 16 13 13 4 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job is completely failed

On Tue, Nov 10, 2015 at 1:55 PM, Tetrajf notifications@github.com wrote:

Ok I'll give that a try. Thanks.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: Glenn Hickey notifications@github.com Date:10/11/2015 8:20 PM (GMT+02:00) To: glennhickey/progressiveCactus progressiveCactus@noreply.github.com Cc: Tetrajf j_featherston@yahoo.com Subject: Re: [progressiveCactus] Bad fasta character (#50)

Pretty weird that even the example doesn't run. Does it work with -database tokyo_cabinet? ie: rm -rf work ; bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal -databse tokyo_cabinet On Tue, Nov 10, 2015 at 10:53 AM, Tetrajf notifications@github.com wrote:

Dear Cactus team. > > Sorry for the dumb error but I'm stuck. I'm getting errors for bad fasta > characters. I have of course removed any non-AGCT characters as well any > lower case symbols. > I will email a log. > Regards > J > > — > Reply to this email directly or view it on GitHub > < https://github.com/glennhickey/progressiveCactus/issues/50>. > —Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/50#issuecomment-155530471 .

Tetrajf commented 8 years ago

Thanks Glen.

Sent from my Samsung Galaxy smartphone.

-------- Original message -------- From: Glenn Hickey notifications@github.com Date:10/11/2015 11:21 PM (GMT+02:00) To: glennhickey/progressiveCactus progressiveCactus@noreply.github.com Cc: Tetrajf j_featherston@yahoo.com Subject: Re: [progressiveCactus] Bad fasta character (#50)

(and original log. unlike blanchette log, where bar is still dying, this one also shows a lastz error complaining about piped in fasta) Got message from job at time: 1447087275.18 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusBarWrapperLarge'> and stats flower name: 4308255993533285646 total bases: 3380315 total-ends: 700 total-caps: 1768 max-end-degree: 21 max-adjacency-length: 47394 total-blocks: 0 total-groups: 1 total-edges: 715 total-free-ends: 138 total-attached-ends: 562 total-chains: 0 total-link groups: 0 The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/log.txt log.txt: -JOBTREE SLAVE OUTPUT LOG- log.txt: FAILURE: bad fasta character in /tmp/stTmp32565_0, >a (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using -ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz -hspthresh=800 -chain -strand=plus -gapped -format=cigar -ambiguous=iupac,100,100 /tmp/stTmp32565_0 /tmp/stTmp32565_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk ' log.txt: log.txt: log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 -minimumOutgroupDegree 0 -alignAmbiguityCharacters -pruneOutStubAlignments -diagonalExpansion 20 -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 with stdin string ' 2008 631770585227063177 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t1/t2/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/log.txt log.txt: -JOBTREE SLAVE OUTPUT LOG- log.txt: FAILURE: bad fasta character in /tmp/stTmp32568_0, >a (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using -ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command echo '>b log.txt: GGCGCGGACGTGGGGGGCCCGGCAGCAGACGCGCAGGACGGCGGCTCCGGCGGCAACGGCACTGACGTGAATGCCTATATCCGGGGGGACTACTCGCTAATGTCGCCCTCGGGCCTGCAGCCCCCCCACTCGCCTTCAGCTCCTTCCTCACAACAACTACCAGGTGCCTCCGGGCATCGGAACACCCCCCAGCAGCAGCCGCAGCCGCAGCAGCAGCGAACCCAGCAGCCACATCCACAACCGGAGCAGGGAGCTAGTCAGCAGCCCCAGCCACACAGGCAGCATCGCCTGTGGGCTTGTAATAACAACAACAATAACAACAACCAGCAGCAGCAATACAGCCATCAAAACCAGCAGCTGGTGTCCACGGGGCATCAGGAGATGCGGAGCTCAGATGACCGTAAGGAAGCTACGGGATCGGGCTCgcagctgcagcagccgcaccaccatcgccatcaccatcaccatcatcataatcaccatcatcatcgccacccccagcatgcga log.txt: ' | cactus_lastz -hspthresh=800 -chain -strand=plus -gapped -format=cigar -ambiguous=iupac,100,100 /tmp/stTmp32568_0 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk ' log.txt: log.txt: log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 -minimumOutgroupDegree 0 -alignAmbiguityCharacters -pruneOutStubAlignments -diagonalExpansion 20 -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 with stdin string ' 2433 631770585227075125 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 496381121429221955 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t0/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/log.txt log.txt: -JOBTREE SLAVE OUTPUT LOG- log.txt: FAILURE: bad fasta character in /tmp/stTmp32570_1, >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using -ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz -hspthresh=800 -chain -strand=plus -gapped -format=cigar -ambiguous=iupac,100,100 /tmp/stTmp32570_0 /tmp/stTmp32570_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk ' log.txt: log.txt: log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 -minimumOutgroupDegree 0 -alignAmbiguityCharacters -pruneOutStubAlignments -diagonalExpansion 20 -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 with stdin string ' 2594 2246451789127745558 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 505529058172318210 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t3/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/log.txt log.txt: -JOBTREE SLAVE OUTPUT LOG- log.txt: FAILURE: bad fasta character in (stdin), >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using -ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command echo '>b log.txt: GGCGGCGTTGACGGGGGTAGGTTGACCGGGGTGACGGGAGTGGGCATGCGCGCATGGGCCCGGATGCTGTATGGCGGGGCCGGTGCACCTGGGTGAGCCTGCCTGATGTATGCGCGGATGCGGATGGGCGACCTGCCACAGCGCCCGGCAGGGGCAAGAGCCACATTGCCGGCATCGCGCGCCACAGTTACTGCAGCTAGCATGAGCTGCCTAGCGTGGCTCTCGGTGTCCGCATGCTCCCATCCTCGTCACCGTTTCCCTGACGCCTACACTTCAGGTCGGGCTAGCGCTGGCGGTAGCTCGCAAGGCCGCGCCGCCCGACTGCATCCGCGCGGCGCTGGACCCGGCCCGGCCGCACATCACGCCACCCACCGCGCCGCCCACTGGCCTGATGATGGTGAGCGCTGGGGCCGCCGCCGCGGA>CACTGAGGACACATGCCACACTGCCGTGTCGTTGTGCCACCAAGTGCACCACTGGGGACACCCCCGCAGCGCCCCGACCTGTAACTGGATGCTTATCTTACTGGTGCAGGAATGGAGCAGGGTAAGGGCGTGGGGAAGGCGCAGGGTGGCGCGGTCCCGATAGTGTGCAGCGTACGATATCCCCGTCTTACTGGTCTTAT log.txt: ' | cactus_lastz -hspthresh=800 -chain -strand=plus -gapped -format=cigar -ambiguous=iupac,100,100 /tmp/stTmp32569_3 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk ' log.txt: log.txt: log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 -minimumOutgroupDegree 0 -alignAmbiguityCharacters -pruneOutStubAlignments -diagonalExpansion 20 -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 with stdin string ' 1231 1128151706656311672 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 1118300082471411968 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host cn04 log.txt: Due to failure we are reducing the remaining retry count of job /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t2/t1/job is completely failed The job seems to have left a log file, indicating failure: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t4/t0/job Reporting file: /scratch/sysusers/Jonathan/progressiveCactus/bin/work/jobTree/jobs/t1/t0/t0/t4/t0/log.txt log.txt: -JOBTREE SLAVE OUTPUT LOG- log.txt: FAILURE: bad fasta character in /tmp/stTmp32598_1, >b (greater than sign ">") log.txt: remove or replace non-ACGTN characters or consider using -ambiguous=iupac log.txt: pclose failed when getting rid of lastz pipe with value 256 and command cactus_lastz -hspthresh=800 -chain -strand=plus -gapped -format=cigar -ambiguous=iupac,100,100 /tmp/stTmp32598_0 /tmp/stTmp32598_1 log.txt: Traceback (most recent call last): log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run log.txt: messages = runBarForTarget(self) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk ' log.txt: log.txt: log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 -minimumOutgroupDegree 0 -alignAmbiguityCharacters -pruneOutStubAlignments -diagonalExpansion 20 -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 with stdin string ' 769 3049640635171594237 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 56154257853759091 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ' exited with non-zero status 1 On Tue, Nov 10, 2015 at 4:19 PM, Glenn Hickey glenn.hickey@gmail.com wrote: > (Pasting some relevant stuff from the files you sent me here so other > developers can see them. I'm stumped) > blanchette example log > > Got message from job at time: 1447171876.38 : Starting bar phase target > with index 0 at 1447171876.1 seconds (recursing = 1) > The job seems to have left a log file, indicating failure: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job > Reporting file: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/log.txt > log.txt: -JOBTREE SLAVE OUTPUT LOG- > log.txt: Read only 0 bytes of string of length 9094 when caching > substrings from DB > log.txt: > log.txt: Traceback (most recent call last): > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", > line 271, in main > log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, > depth=depth) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", > line 153, in execute > log.txt: self.target.run() > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", > line 589, in run > log.txt: messages = runBarForTarget(self) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", > line 583, in runBarForTarget > log.txt: precomputedAlignments=precomputedAlignments) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", > line 326, in runCactusBar > log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, > precomputedAlignments), stdinString=flowerNames) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk > ' > log.txt: database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" > database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" > snapshot="0" /> > log.txt: > log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 > -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 > -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 > -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 > -minimumOutgroupDegree 0 -alignAmbiguityCharacters > -pruneOutStubAlignments -diagonalExpansion 20 > -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 > with stdin string ' 188 9203950263461676184 16 16 16 16 29 16 16 16 16 16 > 16 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 > 16 16 16 16 16 16 16 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 > 29 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 > 16 16 29 16 16 16 16 16 16 16 29 16 16 16 16 4 1 2584 16 16 16 16 16 16 16 > 16 16 16 16 16 16 16 16 16 16 4 3154 13 13 13 13 13 13 13 13 13 13 13 13 13 > 13 4 200 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 16 16 29 4 1320 16 16 > 16 16 16 16 16 16 16 16 16 16 16 16 118 16 16 16 16 16 16 16 16 16 16 16 16 > 16 4 ' exited with non-zero status 1 > log.txt: Exiting the slave because of a failed job on host cn04 > log.txt: Due to failure we are reducing the remaining retry count of job > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job > to 0 > log.txt: We have set the default memory of the failed job to 8589934592 > bytes > Job: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t1/job > is completely failed > The job seems to have left a log file, indicating failure: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job > Reporting file: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/log.txt > log.txt: -JOBTREE SLAVE OUTPUT LOG- > log.txt: Read only 0 bytes of string of length 4259 when caching > substrings from DB > log.txt: > log.txt: Traceback (most recent call last): > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", > line 271, in main > log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, > depth=depth) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/jobTree/scriptTree/stack.py", > line 153, in execute > log.txt: self.target.run() > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", > line 589, in run > log.txt: messages = runBarForTarget(self) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", > line 583, in runBarForTarget > log.txt: precomputedAlignments=precomputedAlignments) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/submodules/cactus/shared/common.py", > line 326, in runCactusBar > log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, > precomputedAlignments), stdinString=flowerNames) > log.txt: File > "/scratch/sysusers/Jonathan/progressiveCactus/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_bar -cactusDisk > ' > log.txt: database_dir="/scratch/sysusers/Jonathan/progressiveCactus/work2/progressiveAlignment/Anc6/Anc6/Anc6_DB" > database_name="Anc6.kch" host="10.128.1.4" in_memory="1" port="1984" > snapshot="0" /> > log.txt: > log.txt: ' -logLevel CRITICAL -spanningTrees 5 -maximumLength 100000 > -gapGamma 0.2 -splitMatrixBiggerThanThis 3000 > -anchorMatrixBiggerThanThis 500 -repeatMaskMatrixBiggerThanThis 500 > -constraintDiagonalTrim 14 -minimumDegree 2 -minimumIngroupDegree 0 > -minimumOutgroupDegree 0 -alignAmbiguityCharacters > -pruneOutStubAlignments -diagonalExpansion 20 > -maximumNumberOfSequencesBeforeSwitchingToFast 10 -largeEndSize 5000 > with stdin string ' 6 9203950263461686172 16 16 13 13 4 ' exited with > non-zero status 1 > log.txt: Exiting the slave because of a failed job on host cn04 > log.txt: Due to failure we are reducing the remaining retry count of job > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job > to 0 > log.txt: We have set the default memory of the failed job to 8589934592 > bytes > Job: > /scratch/sysusers/Jonathan/progressiveCactus/work2/jobTree/jobs/t1/t0/t0/job > is completely failed > > > > > On Tue, Nov 10, 2015 at 1:55 PM, Tetrajf notifications@github.com wrote: > >> Ok I'll give that a try. Thanks. >> >> >> >> Sent from my Samsung Galaxy smartphone. >> >> - Original message - >> From: Glenn Hickey notifications@github.com >> Date:10/11/2015 8:20 PM (GMT+02:00) >> To: glennhickey/progressiveCactus progressiveCactus@noreply.github.com >> Cc: Tetrajf j_featherston@yahoo.com >> Subject: Re: [progressiveCactus] Bad fasta character (#50) >> >> Pretty weird that even the example doesn't run. Does it work with >> -database tokyo_cabinet? ie: rm -rf work ; bin/runProgressiveCactus.sh >> examples/blanchette00.txt ./work ./work/b00.hal -databse tokyo_cabinet On >> Tue, Nov 10, 2015 at 10:53 AM, Tetrajf notifications@github.com wrote: >> > Dear Cactus team. > > Sorry for the dumb error but I'm stuck. I'm getting >> errors for bad fasta > characters. I have of course removed any non-AGCT >> characters as well any > lower case symbols. > I will email a log. > >> Regards > J > > — > Reply to this email directly or view it on GitHub > < >> https://github.com/glennhickey/progressiveCactus/issues/50>. > —Reply to >> this email directly or view it on GitHub. >> >> — >> Reply to this email directly or view it on GitHub >> https://github.com/glennhickey/progressiveCactus/issues/50#issuecomment-155530471 >> . >> > > —Reply to this email directly or view it on GitHub.