Last active
August 29, 2015 14:19
-
-
Save tsackton/92ca44b232d3f952790c to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Logging set at level: DEBUG | |
| Logging to file: test_align.log | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/HUMAN | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/CHIMP | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/BABOON | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/MOUSE | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/RAT | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/DOG | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/CAT | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/PIG | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/COW | |
| Running the command: rm -rf ./testDir/jobTree | |
| Running the command: mkdir ./testDir/sequenceData | |
| Running the command: cactus_createMultiCactusProject.py "/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/expTemplate.xml" "./testDir/progressiveAlignment" --fixNames=0 | |
| Running the command: . /n/home12/tsackton/cuff/progressiveCactus/bin/../src/../environment && cactus_progressive.py --jobTree ./testDir/jobTree --stats --batchSystem "slurm" --maxThreads "60" --maxCpus "1000" --bigBatchSystem "singleMachine" --bigMemoryThreshold "50000000000" --jobTime "20000" --maxLogFileSize "10000000" --slurm-partition "serial_requeue" --slurm-scriptpath "slurm_scripts" --slurm-time "480" ./testDir/progressiveAlignment/progressiveAlignment_project.xml >> ./testDir/cactus.log 2>&1 | |
| Running the command: jobTreeStatus --failIfNotComplete --jobTree ./testDir/jobTree > /dev/null 2>&1 | |
| Error: Command: jobTreeStatus --failIfNotComplete --jobTree ./testDir/jobTree > /dev/null 2>&1 exited with non-zero status 1 | |
| Temporary data was left in: ./testDir | |
| More information can be found in ./testDir/cactus.log | |
| 2015-04-14 10:22:16.741383: Beginning Progressive Cactus Alignment | |
| Got message from job at time: 1429021416.86 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/CAT got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/CAT Total-sequences: 1 Total-length: 50283 Proportion-repeat-masked: 0.228228 ProportionNs: 0.000000 Total-Ns: 0 N50: 50283 Median-sequence-length: 50283 Max-sequence-length: 50283 Min-sequence-length: 50283 | |
| Got message from job at time: 1429021434.83 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/PIG got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/PIG Total-sequences: 1 Total-length: 54843 Proportion-repeat-masked: 0.237751 ProportionNs: 0.000000 Total-Ns: 0 N50: 54843 Median-sequence-length: 54843 Max-sequence-length: 54843 Min-sequence-length: 54843 | |
| Got message from job at time: 1429021452.04 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/HUMAN got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/HUMAN Total-sequences: 1 Total-length: 57553 Proportion-repeat-masked: 0.371710 ProportionNs: 0.000000 Total-Ns: 0 N50: 57553 Median-sequence-length: 57553 Max-sequence-length: 57553 Min-sequence-length: 57553 | |
| Got message from job at time: 1429021452.27 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/CHIMP got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/CHIMP Total-sequences: 1 Total-length: 57344 Proportion-repeat-masked: 0.377337 ProportionNs: 0.000000 Total-Ns: 0 N50: 57344 Median-sequence-length: 57344 Max-sequence-length: 57344 Min-sequence-length: 57344 | |
| Got message from job at time: 1429021452.5 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/BABOON got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/BABOON Total-sequences: 1 Total-length: 58960 Proportion-repeat-masked: 0.384108 ProportionNs: 0.000000 Total-Ns: 0 N50: 58960 Median-sequence-length: 58960 Max-sequence-length: 58960 Min-sequence-length: 58960 | |
| Got message from job at time: 1429021483.63 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/CAT_6 Total-sequences: 1 Total-length: 50283 Proportion-repeat-masked: 0.228228 ProportionNs: 0.000000 Total-Ns: 0 N50: 50283 Median-sequence-length: 50283 Max-sequence-length: 50283 Min-sequence-length: 50283 | |
| Got message from job at time: 1429021497.38 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/MOUSE got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/MOUSE Total-sequences: 1 Total-length: 32750 Proportion-repeat-masked: 0.293344 ProportionNs: 0.000000 Total-Ns: 0 N50: 32750 Median-sequence-length: 32750 Max-sequence-length: 32750 Min-sequence-length: 32750 | |
| Got message from job at time: 1429021503.29 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/COW got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/COW Total-sequences: 1 Total-length: 55508 Proportion-repeat-masked: 0.284536 ProportionNs: 0.000000 Total-Ns: 0 N50: 55508 Median-sequence-length: 55508 Max-sequence-length: 55508 Min-sequence-length: 55508 | |
| Got message from job at time: 1429021516.09 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/HUMAN_0 Total-sequences: 1 Total-length: 57553 Proportion-repeat-masked: 0.371710 ProportionNs: 0.000000 Total-Ns: 0 N50: 57553 Median-sequence-length: 57553 Max-sequence-length: 57553 Min-sequence-length: 57553 | |
| Got message from job at time: 1429021553.65 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/RAT got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/RAT Total-sequences: 1 Total-length: 38436 Proportion-repeat-masked: 0.316526 ProportionNs: 0.000000 Total-Ns: 0 N50: 38436 Median-sequence-length: 38436 Max-sequence-length: 38436 Min-sequence-length: 38436 | |
| Got message from job at time: 1429021560.81 : Before running any preprocessing on the assembly: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/DOG got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /n/home12/tsackton/ratite_scratch/wga/fast_test/cactusTestData/blanchettesSimulation/00.job/DOG Total-sequences: 1 Total-length: 54187 Proportion-repeat-masked: 0.256353 ProportionNs: 0.000000 Total-Ns: 0 N50: 54187 Median-sequence-length: 54187 Max-sequence-length: 54187 Min-sequence-length: 54187 | |
| Got message from job at time: 1429021588.03 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/CHIMP_1 Total-sequences: 1 Total-length: 57344 Proportion-repeat-masked: 0.377337 ProportionNs: 0.000000 Total-Ns: 0 N50: 57344 Median-sequence-length: 57344 Max-sequence-length: 57344 Min-sequence-length: 57344 | |
| Got message from job at time: 1429021601.42 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/MOUSE_3 Total-sequences: 1 Total-length: 32750 Proportion-repeat-masked: 0.293344 ProportionNs: 0.000000 Total-Ns: 0 N50: 32750 Median-sequence-length: 32750 Max-sequence-length: 32750 Min-sequence-length: 32750 | |
| Got message from job at time: 1429021610.35 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/DOG_5 Total-sequences: 1 Total-length: 54187 Proportion-repeat-masked: 0.256353 ProportionNs: 0.000000 Total-Ns: 0 N50: 54187 Median-sequence-length: 54187 Max-sequence-length: 54187 Min-sequence-length: 54187 | |
| Got message from job at time: 1429021631.52 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/RAT_4 Total-sequences: 1 Total-length: 38436 Proportion-repeat-masked: 0.316526 ProportionNs: 0.000000 Total-Ns: 0 N50: 38436 Median-sequence-length: 38436 Max-sequence-length: 38436 Min-sequence-length: 38436 | |
| Got message from job at time: 1429021785.33 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/BABOON_2 Total-sequences: 1 Total-length: 58960 Proportion-repeat-masked: 0.384108 ProportionNs: 0.000000 Total-Ns: 0 N50: 58960 Median-sequence-length: 58960 Max-sequence-length: 58960 Min-sequence-length: 58960 | |
| Got message from job at time: 1429021929.85 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/COW_8 Total-sequences: 1 Total-length: 55508 Proportion-repeat-masked: 0.284536 ProportionNs: 0.000000 Total-Ns: 0 N50: 55508 Median-sequence-length: 55508 Max-sequence-length: 55508 Min-sequence-length: 55508 | |
| Got message from job at time: 1429023074.98 : After preprocessing assembly we got the following stats: Input-sample: ./testDir/sequenceData/PIG_7 Total-sequences: 1 Total-length: 54843 Proportion-repeat-masked: 0.237751 ProportionNs: 0.000000 Total-Ns: 0 N50: 54843 Median-sequence-length: 54843 Max-sequence-length: 54843 Min-sequence-length: 54843 | |
| Got message from job at time: 1429023382.11 : Running blast using the trimming strategy | |
| Got message from job at time: 1429023382.11 : Ingroup sequences: ['/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/renamedInputs/CHIMP_1', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/renamedInputs/HUMAN_0'] | |
| Got message from job at time: 1429023382.11 : Outgroup sequences: ['/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/renamedInputs/BABOON_2', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/renamedInputs/DOG_5', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/renamedInputs/CAT_6'] | |
| Got message from job at time: 1429023382.11 : Blasting ingroups vs outgroups to file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/tmp_mNpijQVpRtunconvertedAlignments | |
| Got message from job at time: 1429023487.97 : Running blast using the trimming strategy | |
| Got message from job at time: 1429023487.97 : Ingroup sequences: ['/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/renamedInputs/COW_8', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/renamedInputs/PIG_7'] | |
| Got message from job at time: 1429023487.97 : Outgroup sequences: ['/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/renamedInputs/DOG_5', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/renamedInputs/CAT_6', '/n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/renamedInputs/HUMAN_0'] | |
| Got message from job at time: 1429023487.97 : Blasting ingroups vs outgroups to file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/tmp_kUameHqFDqunconvertedAlignments | |
| Got message from job at time: 1429023562.95 : Coverage on COW_8 from outgroup #1, DOG_5: 60.5300136917% (current ingroup length 55508, untrimmed length 55508). Outgroup trimmed to 54187 bp from 54187 | |
| Got message from job at time: 1429023562.95 : Coverage on PIG_7 from outgroup #1, DOG_5: 70.1055740933% (current ingroup length 54843, untrimmed length 54843). Outgroup trimmed to 54187 bp from 54187 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 1 outgroups on ingroup COW_8: 60.5300136917 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 1 outgroups on ingroup PIG_7: 70.1055740933 | |
| Got message from job at time: 1429023562.95 : Coverage on COW_8 from outgroup #2, CAT_6: 25.2618574421% (current ingroup length 18617, untrimmed length 55508). Outgroup trimmed to 34588 bp from 50283 | |
| Got message from job at time: 1429023562.95 : Coverage on PIG_7 from outgroup #2, CAT_6: 31.8123116659% (current ingroup length 11615, untrimmed length 54843). Outgroup trimmed to 34588 bp from 50283 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 2 outgroups on ingroup COW_8: 68.4910283202 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 2 outgroups on ingroup PIG_7: 76.5184253232 | |
| Got message from job at time: 1429023562.95 : Coverage on COW_8 from outgroup #3, HUMAN_0: 5.11479881791% (current ingroup length 13197, untrimmed length 55508). Outgroup trimmed to 17113 bp from 57553 | |
| Got message from job at time: 1429023562.95 : Coverage on PIG_7 from outgroup #3, HUMAN_0: 19.4097460535% (current ingroup length 7285, untrimmed length 54843). Outgroup trimmed to 17113 bp from 57553 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 3 outgroups on ingroup COW_8: 69.5719535923 | |
| Got message from job at time: 1429023562.95 : Cumulative coverage of 3 outgroups on ingroup PIG_7: 78.9526466459 | |
| Got message from job at time: 1429023749.6 : Coverage on CHIMP_1 from outgroup #1, BABOON_2: 95.849609375% (current ingroup length 57344, untrimmed length 57344). Outgroup trimmed to 58960 bp from 58960 | |
| Got message from job at time: 1429023749.6 : Coverage on HUMAN_0 from outgroup #1, BABOON_2: 95.548450993% (current ingroup length 57553, untrimmed length 57553). Outgroup trimmed to 58960 bp from 58960 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 1 outgroups on ingroup CHIMP_1: 95.849609375 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 1 outgroups on ingroup HUMAN_0: 95.548450993 | |
| Got message from job at time: 1429023749.6 : Coverage on CHIMP_1 from outgroup #2, DOG_5: 4.475781729% (current ingroup length 1631, untrimmed length 57344). Outgroup trimmed to 4073 bp from 54187 | |
| Got message from job at time: 1429023749.6 : Coverage on HUMAN_0 from outgroup #2, DOG_5: 4.04880754298% (current ingroup length 1803, untrimmed length 57553). Outgroup trimmed to 4073 bp from 54187 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 2 outgroups on ingroup CHIMP_1: 95.9769112723 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 2 outgroups on ingroup HUMAN_0: 95.6752906017 | |
| Got message from job at time: 1429023749.6 : Coverage on CHIMP_1 from outgroup #3, CAT_6: 0% (current ingroup length 1556, untrimmed length 57344). Outgroup trimmed to 0 bp from 50283 | |
| Got message from job at time: 1429023749.6 : Coverage on HUMAN_0 from outgroup #3, CAT_6: 0% (current ingroup length 1728, untrimmed length 57553). Outgroup trimmed to 0 bp from 50283 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 3 outgroups on ingroup CHIMP_1: 95.9769112723 | |
| Got message from job at time: 1429023749.6 : Cumulative coverage of 3 outgroups on ingroup HUMAN_0: 95.6752906017 | |
| Got message from job at time: 1429023772.14 : Blocking on ktserver <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" in_memory="1" port="1984" snapshot="1" /> | |
| with killPath /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/tmp_RvGfMK1ijY_kill.txt | |
| Got message from job at time: 1429023832.52 : Converted headers of cigar file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/gTD3/tmp_9pI7Py5XsO/tmp_kUameHqFDqunconvertedAlignments to internal names, new file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/gTD1/tmp_hVGmkge1pl/tmp_jfqAvm2tE2 | |
| Got message from job at time: 1429023832.52 : Starting caf phase target with index 0 at 1429023812.08 seconds (recursing = 1) | |
| Got message from job at time: 1429023839.59 : Starting bar phase target with index 0 at 1429023834.68 seconds (recursing = 1) | |
| Got message from job at time: 1429024160.14 : Blocking on ktserver <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc7/Anc7/Anc7_DB" database_name="Anc7.kch" in_memory="1" port="1985" snapshot="1" /> | |
| with killPath /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/tmp_US9vluAXeO_kill.txt | |
| Got message from job at time: 1429024237.96 : Starting avg phase target with index 0 at 1429024062.62 seconds (recursing = 0) | |
| Got message from job at time: 1429024237.96 : Starting reference phase target with index 0 at 1429024062.77 seconds (recursing = 1) | |
| Got message from job at time: 1429024271.32 : Converted headers of cigar file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/gTD2/tmp_kFTtPYzHHu/tmp_mNpijQVpRtunconvertedAlignments to internal names, new file /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/gTD1/tmp_YtY2LwNQme/tmp_mN0fRf7Rok | |
| Got message from job at time: 1429024271.32 : Starting caf phase target with index 0 at 1429024195.64 seconds (recursing = 1) | |
| Got message from job at time: 1429024275.68 : Starting bar phase target with index 0 at 1429024273.52 seconds (recursing = 1) | |
| Got message from job at time: 1429024333.67 : Blocking on ktserver <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc6/Anc6/Anc6_DB_tempSecondaryDatabaseDir_0.553148945999" database_name="Anc6.kch" in_memory="1" port="2084" snapshot="1" /> | |
| with killPath /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/gTD1/tmp_hVGmkge1pl/tmp_oyYlazX2A3_kill.txt | |
| The job seems to have left a log file, indicating failure: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t0/job | |
| Reporting file: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t0/log.txt | |
| log.txt: ---JOBTREE SLAVE OUTPUT LOG--- | |
| log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: 10.31.129.2 with error: network error | |
| log.txt: Uncaught exception | |
| log.txt: Traceback (most recent call last): | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main | |
| log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute | |
| log.txt: self.target.run() | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 560, in run | |
| log.txt: self.makeRecursiveTargets() | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 236, in makeRecursiveTargets | |
| log.txt: default=CactusRecursionTarget.maxSequenceSizeOfFlowerGroupingDefault)) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/shared/common.py", line 78, in runCactusGetFlowers | |
| log.txt: stdinString=flowerNames) | |
| log.txt: File "/n/home12/tsackton/cuff/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_workflow_getFlowers CRITICAL '<st_kv_database_conf type="kyoto_tycoon"> | |
| log.txt: <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc7/Anc7/Anc7_DB" database_name="Anc7.kch" host="10.31.129.2" in_memory="1" port="1985" snapshot="1" /> | |
| log.txt: </st_kv_database_conf> | |
| log.txt: ' 0 100000000 1000000 with stdin string ' 5 985162418487319 1224 254 824 262 ' exited with non-zero status 128 | |
| log.txt: Exiting the slave because of a failed job on host holyconroy06.rc.fas.harvard.edu | |
| log.txt: Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t0/job to 0 | |
| log.txt: We have set the default memory of the failed job to 34359738368 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t0/job is completely failed | |
| The job seems to have left a log file, indicating failure: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t1/job | |
| Reporting file: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t1/log.txt | |
| log.txt: ---JOBTREE SLAVE OUTPUT LOG--- | |
| log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: 10.31.129.2 with error: network error | |
| log.txt: Uncaught exception | |
| log.txt: Traceback (most recent call last): | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main | |
| log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute | |
| log.txt: self.target.run() | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 589, in run | |
| log.txt: messages = runBarForTarget(self) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 583, in runBarForTarget | |
| log.txt: precomputedAlignments=precomputedAlignments) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/shared/common.py", line 326, in runCactusBar | |
| log.txt: largeEndSize, endAlignmentsToPrecomputeOutputFile, precomputedAlignments), stdinString=flowerNames) | |
| log.txt: File "/n/home12/tsackton/cuff/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 '<st_kv_database_conf type="kyoto_tycoon"> | |
| log.txt: <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc7/Anc7/Anc7_DB" database_name="Anc7.kch" host="10.31.129.2" in_memory="1" port="1985" snapshot="1" /> | |
| log.txt: </st_kv_database_conf> | |
| 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 ' 269 985162418487303 40 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 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 46 16 16 16 16 16 16 16 16 16 16 16 16 16 40 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 16 16 16 16 16 16 16 16 16 54 16 16 16 16 16 16 16 16 16 16 16 16 16 57 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 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 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 ' exited with non-zero status 128 | |
| log.txt: Exiting the slave because of a failed job on host wofsy013.rc.fas.harvard.edu | |
| log.txt: Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t1/job to 0 | |
| log.txt: We have set the default memory of the failed job to 4294967296 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t1/t1/job is completely failed | |
| The job seems to have left a log file, indicating failure: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t1/job | |
| Reporting file: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t1/log.txt | |
| log.txt: ---JOBTREE SLAVE OUTPUT LOG--- | |
| log.txt: Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: 10.31.128.211 with error: network error | |
| log.txt: Uncaught exception | |
| log.txt: Traceback (most recent call last): | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main | |
| log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute | |
| log.txt: self.target.run() | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/pipeline/cactus_workflow.py", line 777, in run | |
| log.txt: makeScaffolds=self.getOptionalPhaseAttrib("makeScaffolds", bool)) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/cactus/shared/common.py", line 363, in runCactusReference | |
| log.txt: popenPush(command, stdinString=flowerNames) | |
| log.txt: File "/n/home12/tsackton/cuff/progressiveCactus/submodules/sonLib/bioio.py", line 223, in popenPush | |
| log.txt: raise RuntimeError("Command: %s with stdin string '%s' exited with non-zero status %i" % (command, stdinString, sts)) | |
| log.txt: RuntimeError: Command: cactus_reference --cactusDisk '<st_kv_database_conf type="kyoto_tycoon"> | |
| log.txt: <kyoto_tycoon database_dir="/n/regal/edwards_lab/ratites/wga/fast_test/testDir/progressiveAlignment/Anc6/Anc6/Anc6_DB" database_name="Anc6.kch" host="10.31.128.211" in_memory="1" port="1984" snapshot="1" /> | |
| log.txt: </st_kv_database_conf> | |
| log.txt: ' --logLevel CRITICAL --matchingAlgorithm blossom5 --referenceEventString Anc6 --permutations 10 --useSimulatedAnnealing --theta 0.0001 --maxWalkForCalculatingZ 100000 --ignoreUnalignedGaps --wiggle 0.9999 --numberOfNs 10 --minNumberOfSequencesToSupportAdjacency 1 --makeScaffolds with stdin string '1 0' exited with non-zero status 128 | |
| log.txt: Exiting the slave because of a failed job on host holy2a15206.rc.fas.harvard.edu | |
| log.txt: Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t1/job to 0 | |
| log.txt: We have set the default memory of the failed job to 34359738368 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t1/job is completely failed | |
| Batch system is reporting that the job (1, 45) /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t0/job failed with exit value 1 | |
| No log file is present, despite job failing: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t0/job | |
| Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t0/job to 0 | |
| We have set the default memory of the failed job to 34359738368 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t1/t0/job is completely failed | |
| Batch system is reporting that the job (1, 32) /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t0/job failed with exit value 1 | |
| No log file is present, despite job failing: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t0/job | |
| Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t0/job to 0 | |
| We have set the default memory of the failed job to 34359738368 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t0/t0/job is completely failed | |
| Batch system is reporting that the job (1, 39) /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t0/job failed with exit value 1 | |
| g file is present, despite job failing: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t0/job | |
| Due to failure we are reducing the remaining retry count of job /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t0/job to 0 | |
| We have set the default memory of the failed job to 34359738368 bytes | |
| Job: /n/home12/tsackton/ratite_scratch/wga/fast_test/testDir/jobTree/jobs/t1/t0/job is completely failed | |
| 2015-04-14 21:42:24.347167: Finished Progressive Cactus Alignment |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment