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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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not exporting .hal file #10

Closed Mcfoofa closed 10 years ago

Mcfoofa commented 10 years ago

When running the progessiveCactus aligner,

bin/runProgressiveCactus.sh examples/drosophila_2R.txt ./2R ./2R/b00.hal

no .hal file is created in the 2R folder. This is what results at the end of the cactus.log file.

2013-12-15 00:13:33.608623: Beginning HAL Export

hal exception caught: Error opening/home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc0/Anc0_hal.c2h Command exited with non-zero status 1 0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 10816maxresident)k 0inputs+0outputs (0major+740minor)pagefaults 0swaps rm -f ./2R/b00.hal: time halAppendCactusSubtree '/home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc0/Anc0_hal.c2h' '/home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc0/Anc0_hal.fa' '(Anc2:3.0,Anc1:6.0)Anc0;' './2R/b00.hal:' Traceback (most recent call last): File "/home/hussainather/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 122, in main(); File "/home/hussainather/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 113, in main system(cmdline) File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 171, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: time halAppendCactusSubtree '/home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc0/Anc0_hal.c2h' '/home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc0/Anc0_hal.fa' '(Anc2:3.0,Anc1:6.0)Anc0;' './2R/b00.hal:' exited with non-zero status 1

joelarmstrong commented 10 years ago

Were there any errors before this in the log? It looks like it can't find a file that is created in a previous step.

Mcfoofa commented 10 years ago

This is what it said before:

2013-12-14 23:35:47.494785: Beginning Progressive Cactus Alignment

Got message from job at time: 1387082653.73 : Blocking on ktserver with killPath /home/hussainather/progressiveCactus/2R/jobTree/jobs/gTD4/tmp_F6C6Me1ErI/tmp_980iFvabtH_kill.txt Got message from job at time: 1387082655.06 : Input-sample: ./2R/sequenceData/dere_2R.fasta Total-sequences: 3 Total-length: 22480453 Proportion-repeat-masked: 0.008739 ProportionNs: 0.000069 N50: 195375 Median-sequence-length: 1488 Got message from job at time: 1387082655.06 : Input-sample: ./2R/sequenceData/dyak_2R.fasta Total-sequences: 1 Total-length: 21047017 Proportion-repeat-masked: 0.006241 ProportionNs: 0.000156 N50: 131362 Median-sequence-length: 21047017 Got message from job at time: 1387082655.06 : Input-sample: ./2R/sequenceData/dmel-2R-chromosome-r5.54.fasta Total-sequences: 1 Total-length: 21146708 Proportion-repeat-masked: 0.003176 ProportionNs: 0.000005 N50: 67165 Median-sequence-length: 21146708 Got message from job at time: 1387082655.06 : Starting caf phase target with index 0 at 1387082654.69 seconds (recursing = 1) Got message from job at time: 1387082655.06 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusCafWrapperLarge'> and stats flower name: 0 total bases: 64674178 total-ends: 10 total-caps: 10 max-end-degree: 1 max-adjacency-length: 22477793 total-blocks: 0 total-groups: 1 total-edges: 5 total-free-ends: 10 total-attached-ends: 0 total-chains: 0 total-link groups: 0 Got message from job at time: 1387083546.03 : Pinch graph component with 1621 nodes and 1892 edges is being split up by breaking 182 edges to reduce size to less than 652 max, but found 0 pointless edges Got message from job at time: 1387083546.03 : Attaching the sequence to the cactus root 129759964263611499, header scaffold_4845 with length 22477792 and 14937036 total bases aligned and 0 bases aligned to other chromosome threads Got message from job at time: 1387083546.17 : Starting bar phase target with index 0 at 1387083546.06 seconds (recursing = 1) Got message from job at time: 1387083611.23 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusBarWrapperLarge'> and stats flower name: 1215549686924969117 total bases: 1265649 total-ends: 363 total-caps: 1034 max-end-degree: 19 max-adjacency-length: 116105 total-blocks: 0 total-groups: 1 total-edges: 388 total-free-ends: 0 total-attached-ends: 363 total-chains: 0 total-link groups: 0 Got message from job at time: 1387083611.23 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusBarWrapperLarge'> and stats flower name: 1215549686924969965 total bases: 3116004 total-ends: 774 total-caps: 2274 max-end-degree: 19 max-adjacency-length: 414590 total-blocks: 0 total-groups: 1 total-edges: 823 total-free-ends: 0 total-attached-ends: 774 total-chains: 0 total-link groups: 0 Got message from job at time: 1387083611.23 : Adding an oversize flower for target class <class 'cactus.pipeline.cactus_workflow.CactusBarWrapperLarge'> and stats flower name: 1215549686924969969 total bases: 2671270 total-ends: 772 total-caps: 2446 max-end-degree: 23 max-adjacency-length: 156505 total-blocks: 0 total-groups: 1 total-edges: 798 total-free-ends: 3 total-attached-ends: 769 total-chains: 0 total-link groups: 0 Got message from job at time: 1387083612.62 : Breaking bar job into 3 separate jobs Got message from job at time: 1387083657.15 : Breaking bar job into 6 separate jobs Got message from job at time: 1387083657.21 : Breaking bar job into 5 separate jobs The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/ktserverJobTree.py", line 139, in run log.txt: killPingInterval=self.runTimestep) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/ktserverControl.py", line 129, in runKtserver log.txt: raise e log.txt: RuntimeError: ktserver finished before it could be killed with the file. Server log is: /home/hussainather/progressiveCactus/2R/progressiveAlignment/Anc2/Anc2/Anc2_DB/ktout.log log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t0/t1/t3/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t0/t1/t3/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t0/t1/gTD0/tmp_YeunJ8wZjL/endAlignments.5 with stdin string '10 1215549686924969965 7605313133233512973 392516855023012478 17 40 85 491 59 268 131' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t0/t1/t3/t0/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t0/t1/t3/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/gTD0/tmp_V6QiJUMU5E/endAlignments.0 with stdin string '36 1215549686924969969 -1085789722661358447 249527566854003059 158 694 6762 427 242490692436213364 17 328481297821340331 79 450 3309 682 48 35 510 683 293 96 35 285 130041439240307888 13596 52635820644880872 213 76 17 354 19 305 80924055804313000 1596 8083 20969885764936820 60' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t0/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t1/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/gTD0/tmp_V6QiJUMU5E/endAlignments.1 with stdin string '55 1215549686924969969 19281035904676024 401 5157 137 1353894637978233186 749 111 92 77 435 73 331 52072870691470798 77 109 99 1052 14 246 121 7526 894 524247144123581255 77 137 9 362 304 11141 20 35325109577178627 6 89 92 642748109318786644 254 527 70 60 17 71 41 353 125 667799382246027602 72 359443545259492896 142 98516241848728753 23 9 279 9446 92' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t1/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t0/t1/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t1/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t1/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/gTD0/tmp_V6QiJUMU5E/endAlignments.2 with stdin string '46 1215549686924969969 3805260210151323979 323 261 581 10336 165366548817505036 1111 298 126523002031430361 131 301 61 1931 134 7845 699 235 620652323646977457 77 283 602 274 139 1361 542261542633074728 294563563127698048 118 8303 28 17 1047 58 34 799 143 1854 192 752 348184546191080637 6 29695610042959077 517 2423 110 107' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t1/t0/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t1/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t2/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t2/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/gTD0/tmp_V6QiJUMU5E/endAlignments.3 with stdin string '42 1215549686924969969 5932507346642092863 359443545259502288 372 1332 382 100 37576909390868598 148 87 10292 238550042762284867 21814310695068274 152700174865525753 9116 570 65 335377434750740575 93 244 522 108 17 179 187 1840 76 170 46 1113 251 147 376 101049516639115539 293015450755784683 162 26 197 167 23 505 133278401472496054' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t2/t0/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t2/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t3/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t3/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 549, in run log.txt: endAlignmentsToPrecomputeOutputFile=self.alignmentFile) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --endAlignmentsToPrecomputeOutputFile /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/gTD0/tmp_V6QiJUMU5E/endAlignments.4 with stdin string '17 1215549686924969969 7605313133233508812 1007 61 3106 6 290622913453742461 148 236 44 17 3879 650 196 556 190 77' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t3/t0/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t1/t1/t0/t3/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 462, in run log.txt: self.makeRecursiveTargets() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 240, in makeRecursiveTargets log.txt: default=CactusRecursionTarget.maxSequenceSizeOfFlowerGroupingDefault)) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 78, in runCactusGetFlowers log.txt: stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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_workflow_getFlowers CRITICAL ' log.txt: log.txt: log.txt: ' 0 100000000 1000000 with stdin string ' 3 1812558112528264727 4039728865751308770 374 ' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t0/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t1/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 491, in run log.txt: messages = runBarForTarget(self) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 ' 346 437130638831660225 13 13 4 82331430687862063 16 16 16 16 4 2026 325385073077511196 16 16 16 16 16 4 335940384704170336 16 4 286682263779789959 6918 13 13 13 13 13 13 13 35 19 19 19 19 19 4 1 345088321447261623 19 19 4 173 4 1996361272320311536 13 13 13 4 3735 19 19 19 19 4 105975328731551716 16 16 16 16 16 16 16 16 16 16 16 29 16 16 16 4 157 16 16 4 155514924632641652 19 23 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 4 1 656118170712528650 67413256922207396 19 4 748441963073624307 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 16 16 16 16 16 16 16 16 16 16 16 16 16 16 4 201395345836478664 13 13 4 5944 16 16 16 13 51228445761335396 13 13 13 4 143 16 16 16 16 4 57280157760616477 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 35 19 19 4 1 291 13 13 13 13 262 13 13 13 13 35 19 159 19 4 1 615304299089479247 16 16 16 16 16 16 16 16 16 16 16 16 16 4 157 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 4 43 4 90071992547413869 23 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 23 13 13 13 13 13 13 29 16 4 1 4843 13 13 13 13 13 13 13 13 13 13 4 1 212513607416546236 4 1523342573958049480 19 19 29 16 16 16 16 16 16 16 16 16 16 4 ' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t1/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t1/t0/t0/t1/job is completely failed The job seems to have left a log file, indicating failure: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/job Reporting file: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: hahnlab-pc01 with error: network error log.txt: Uncaught exception log.txt: Traceback (most recent call last): log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/hussainather/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 558, in run log.txt: messages = runBarForTarget(self, precomputedAlignments=self.phaseNode.attrib["precomputedAlignmentFiles"]) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 485, in runBarForTarget log.txt: precomputedAlignments=precomputedAlignments) log.txt: File "/home/hussainather/progressiveCactus/submodules/cactus/shared/common.py", line 315, in runCactusBar log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) log.txt: File "/home/hussainather/progressiveCactus/submodules/sonLib/bioio.py", line 198, 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 --precomputedAlignments '/home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/gTD0/tmp_VHPvdhUbPs/endAlignments.0 /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/gTD0/tmp_VHPvdhUbPs/endAlignments.1 /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/gTD0/tmp_VHPvdhUbPs/endAlignments.2' with stdin string ' 1 1215549686924969117 ' exited with non-zero status 128 log.txt: Exiting the slave because of a failed job on host hahnlab-pc01 log.txt: Due to failure we are reducing the remaining retry count of job /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /home/hussainather/progressiveCactus/2R/jobTree/jobs/t1/t0/t0/t3/t0/job is completely failed

2013-12-15 00:13:33.605586: Finished Progressive Cactus Alignment

Mcfoofa commented 10 years ago

Never mind. It's working now. Not sure what the problem was.