benedictpaten/assemblaScripts — Issue #2: make testLittle failed
Author: ravinkazo
Created: 2012-01-07 15:33:14+00:00
State: open

Hello!
Could you help me please?
I've installed all the required dependencies and made sure that they're paths are correct, but I kept getting errors when I ran make testLittle. I've tried looking everywhere for solution but I couldn't find any. Would really appreciate it if you could address this. Many thanks!

make testLittle
cd tests/little && make all
make[1]: Entering directory `/home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little'
rm -rf ./jobTree
#Running pipeline to build comparisons
python ../../bin/pipeline.py --geneBedFiles '../../data/tests/little/beds/test1.bed' --featureBedFiles '../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed' --assemblyEventString assembly --haplotype1EventString hapA1 --haplotype2EventString hapA2 --contaminationEventString ecoli --haplotypeSequences '../../data/assemblathon1/simulatedHaplotypes/Escherichia_coliO83_H1_1.trf.repmask.fa.complete ../../data/assemblathon1/simulatedHaplotypes/Escherichia_coliO83_H1_1.trf.repmask.fa.complete ../../data/assemblathon1/simulatedHaplotypes/Escherichia_coliO83_H1_1.trf.repmask.fa.complete' --newickTree '(((hapA1:0.002,hapA2:0.002):0.0000001,ecoli:0.002):0.000001,assembly:0.002);' --assembliesDir ../../data/tests/little --outputDir ../../output/tests/little --configFile ../../lib/config_fast.xml --minimumNsForScaffoldGap 15 --jobTree ./jobTree --batchSystem singleMachine --maxThreads 10 --logDebug --retryCount 0
Logging set at level: DEBUG
Logging to file: None
Logging set at level: DEBUG
Logging to file: None
Starting to create the job tree setup for the first time
Using the single machine batch system
Written the config file
We have setup the temp file tree, it contains 0 files currently, 0.0 of the possible total
We have setup the temp file tree, it contains 0 files currently, 0.0 of the possible total
We have setup the temp file tree, it contains 0 files currently, 0.0 of the possible total
We have setup the temp file tree, it contains 0 files currently, 0.0 of the possible total
Setup the temp file trees
Finished the job tree setup
Adding the first job
Added the first job
Written the environment for the jobs to the environment file
Got parameters, wait duration 0.0, rescue jobs frequency: 1800.0 max job duration: 9.22337203685e+18
Checked batch system has no running jobs and no updated jobs
Got a list of job files
Fixed the job files using any .old files
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Restarting job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Reworked failed jobs
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Got the active (non blue) job files
Starting the main loop
Built the jobs list, currently have 1 job files, 1 jobs to update and 0 jobs currently issued
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with memory: 2147483648, cpu: 1
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with job id: 0 and cpus: 1
Starting a job with ID 0
Running the command: mv /tmp/tmpTJrYHV /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_sSZX7ckVmz.log
Finished a job with ID 0
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with exit value: 0
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml to active jobs
Built the jobs list, currently have 1 job files, 1 jobs to update and 0 jobs currently issued
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has finished okay
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has a new command that we can now issue
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with memory: 8000000000, cpu: 1
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with job id: 1 and cpus: 1
Starting a job with ID 1
Running the command: mv /tmp/tmpw7E01b /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_sSZX7ckVmz.log
Finished a job with ID 1
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with exit value: 0
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml to active jobs
Built the jobs list, currently have 1 job files, 1 jobs to update and 0 jobs currently issued
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has finished okay
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has a new command that we can now issue
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with memory: 8000000000, cpu: 4
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with job id: 2 and cpus: 4
Starting a job with ID 2
Running the command: mv /tmp/tmpBoVPYl /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_sSZX7ckVmz.log
Finished a job with ID 2
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml with exit value: 0
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml to active jobs
Built the jobs list, currently have 1 job files, 1 jobs to update and 0 jobs currently issued
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has finished okay
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_7RWet6kS8h.xml has 3 children to schedule
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml with memory: 8000000000, cpu: 4
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml with memory: 8000000000, cpu: 4
Issuing the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml with memory: 8000000000, cpu: 4
Starting a job with ID 3
Starting a job with ID 4
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml with job id: 3 and cpus: 4
Starting a job with ID 5
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml with job id: 4 and cpus: 4
Issued the job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml with job id: 5 and cpus: 4
Running the command: mv /tmp/tmpnf_jgj /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_ViRB4pW9uK.log
Running the command: mv /tmp/tmpxk7MOB /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_iQVZulCup6.log
Running the command: mv /tmp/tmpnJIcb3 /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_SGouo838Ts.log
Finished a job with ID 4
Finished a job with ID 5
Finished a job with ID 3
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml with exit value: 0
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml with exit value: 0
Ran the command: /usr/bin/python -E /home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave /home/ravinkazo/ASSEMBLATHON --job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml with exit value: 0
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml to active jobs
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml to active jobs
Batch system is reporting that the job /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml ended successfully
Added job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml to active jobs
Built the jobs list, currently have 4 job files, 3 jobs to update and 0 jobs currently issued
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml failed
The log file of the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_n96cz2W6O1.log
tmp_n96cz2W6O1.log:	Loading the class name assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_n96cz2W6O1.log:	Setup logging with level: DEBUG
tmp_n96cz2W6O1.log:	Running the command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed
tmp_n96cz2W6O1.log:	Traceback (most recent call last):
tmp_n96cz2W6O1.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave", line 119, in processJob
tmp_n96cz2W6O1.log:	jobTree.scriptTree.scriptTree.run(tempJob, l[1], l[2:])
tmp_n96cz2W6O1.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/scriptTree.py", line 42, in run
tmp_n96cz2W6O1.log:	target.execute(job)
tmp_n96cz2W6O1.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/stack.py", line 218, in execute
tmp_n96cz2W6O1.log:	target.run()
tmp_n96cz2W6O1.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/pipeline.py", line 236, in run
tmp_n96cz2W6O1.log:	system("python %s/bedFileIntersection.py %s %s %s" % (binPath, contigPathOutputFile, contigPathOverlapFile, self.options.featureBedFiles))
tmp_n96cz2W6O1.log:	File "/home/ravinkazo/ASSEMBLATHON/sonLib/bioio.py", line 158, in system
tmp_n96cz2W6O1.log:	raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
tmp_n96cz2W6O1.log:	RuntimeError: Command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed exited with non-zero status 1
The log file of the slave for the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_ViRB4pW9uK.log
tmp_ViRB4pW9uK.log:	Parsed arguments and set up logging
tmp_ViRB4pW9uK.log:	Loaded the environment for the process
tmp_ViRB4pW9uK.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_qaL5TWf44I/4/tmp_PTkfFMBKeb.pickle assemblaScripts.bin.pipeline.MakeCoveragePlots with exit status 0
tmp_ViRB4pW9uK.log:	Passed the job, okay
tmp_ViRB4pW9uK.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/1/tmp_vRT1QXmF8E.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats
tmp_ViRB4pW9uK.log:	Making a stub follow on job
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq/localTempDir/*
tmp_ViRB4pW9uK.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_ViRB4pW9uK.log:	Updated the status of the job to grey and starting the next job
tmp_ViRB4pW9uK.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/1/tmp_vRT1QXmF8E.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats with exit status 0
tmp_ViRB4pW9uK.log:	Passed the job, okay
tmp_ViRB4pW9uK.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/2/tmp_2N0cGUFz9H.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats
tmp_ViRB4pW9uK.log:	Making a stub follow on job
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq/localTempDir/*
tmp_ViRB4pW9uK.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_ViRB4pW9uK.log:	Updated the status of the job to grey and starting the next job
tmp_ViRB4pW9uK.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/2/tmp_2N0cGUFz9H.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats with exit status 0
tmp_ViRB4pW9uK.log:	Passed the job, okay
tmp_ViRB4pW9uK.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/3/tmp_QH8S2ycZPG.pickle assemblaScripts.bin.pipeline.MakeLinkageStats
tmp_ViRB4pW9uK.log:	Making a stub follow on job
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq/localTempDir/*
tmp_ViRB4pW9uK.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_ViRB4pW9uK.log:	Updated the status of the job to grey and starting the next job
tmp_ViRB4pW9uK.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/3/tmp_QH8S2ycZPG.pickle assemblaScripts.bin.pipeline.MakeLinkageStats with exit status 0
tmp_ViRB4pW9uK.log:	Passed the job, okay
tmp_ViRB4pW9uK.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/4/tmp_fLk2oIZ29e.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_ViRB4pW9uK.log:	Making a stub follow on job
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq/localTempDir/*
tmp_ViRB4pW9uK.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_ViRB4pW9uK.log:	Updated the status of the job to grey and starting the next job
tmp_ViRB4pW9uK.log:	Traceback (most recent call last):
tmp_ViRB4pW9uK.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 71, in
tmp_ViRB4pW9uK.log:	samples, complete, totalLength, totalContainment = getContainment(pathIntervals, parseBedFile(bedFile))
tmp_ViRB4pW9uK.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 8, in parseBedFile
tmp_ViRB4pW9uK.log:	intervals = [ fn(line.split()[:3]) for line in open(file, 'r').readlines() ]
tmp_ViRB4pW9uK.log:	IOError: [Errno 2] No such file or directory: '../../data/tests/little/beds/test1.bed'
tmp_ViRB4pW9uK.log:	Caught an exception in the target being run
tmp_ViRB4pW9uK.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_Fcm3GwkVeS/4/tmp_fLk2oIZ29e.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals with exit status 1
tmp_ViRB4pW9uK.log:	Failed the job
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq/localTempDir/*
tmp_ViRB4pW9uK.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_ViRB4pW9uK.log:	Exiting the slave because of a failed job
tmp_ViRB4pW9uK.log:	Running the command: mv /tmp/tmpJHwkpq/temp.log /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_n96cz2W6O1.log
tmp_ViRB4pW9uK.log:	Written out an updated job file
tmp_ViRB4pW9uK.log:	Finished running the chain of jobs on this node, we ran for a total of 0.063525 seconds
tmp_ViRB4pW9uK.log:	Running the command: rm -rf /tmp/tmpJHwkpq
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_3Nl98WGHhU.xml is completely failed
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml failed
The log file of the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_f4KjSp3MBS.log
tmp_f4KjSp3MBS.log:	Loading the class name assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_f4KjSp3MBS.log:	Setup logging with level: DEBUG
tmp_f4KjSp3MBS.log:	Running the command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed
tmp_f4KjSp3MBS.log:	Traceback (most recent call last):
tmp_f4KjSp3MBS.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave", line 119, in processJob
tmp_f4KjSp3MBS.log:	jobTree.scriptTree.scriptTree.run(tempJob, l[1], l[2:])
tmp_f4KjSp3MBS.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/scriptTree.py", line 42, in run
tmp_f4KjSp3MBS.log:	target.execute(job)
tmp_f4KjSp3MBS.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/stack.py", line 218, in execute
tmp_f4KjSp3MBS.log:	target.run()
tmp_f4KjSp3MBS.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/pipeline.py", line 236, in run
tmp_f4KjSp3MBS.log:	system("python %s/bedFileIntersection.py %s %s %s" % (binPath, contigPathOutputFile, contigPathOverlapFile, self.options.featureBedFiles))
tmp_f4KjSp3MBS.log:	File "/home/ravinkazo/ASSEMBLATHON/sonLib/bioio.py", line 158, in system
tmp_f4KjSp3MBS.log:	raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
tmp_f4KjSp3MBS.log:	RuntimeError: Command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed exited with non-zero status 1
The log file of the slave for the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_SGouo838Ts.log
tmp_SGouo838Ts.log:	Parsed arguments and set up logging
tmp_SGouo838Ts.log:	Loaded the environment for the process
tmp_SGouo838Ts.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_qaL5TWf44I/4/tmp_RtMTgxLhVe.pickle assemblaScripts.bin.pipeline.MakeCoveragePlots with exit status 0
tmp_SGouo838Ts.log:	Passed the job, okay
tmp_SGouo838Ts.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/1/tmp_mhpL3gC7bl.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats
tmp_SGouo838Ts.log:	Making a stub follow on job
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR/localTempDir/*
tmp_SGouo838Ts.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_SGouo838Ts.log:	Updated the status of the job to grey and starting the next job
tmp_SGouo838Ts.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/1/tmp_mhpL3gC7bl.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats with exit status 0
tmp_SGouo838Ts.log:	Passed the job, okay
tmp_SGouo838Ts.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/2/tmp_XiFVHD2Kwz.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats
tmp_SGouo838Ts.log:	Making a stub follow on job
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR/localTempDir/*
tmp_SGouo838Ts.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_SGouo838Ts.log:	Updated the status of the job to grey and starting the next job
tmp_SGouo838Ts.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/2/tmp_XiFVHD2Kwz.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats with exit status 0
tmp_SGouo838Ts.log:	Passed the job, okay
tmp_SGouo838Ts.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/3/tmp_ildndCIquW.pickle assemblaScripts.bin.pipeline.MakeLinkageStats
tmp_SGouo838Ts.log:	Making a stub follow on job
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR/localTempDir/*
tmp_SGouo838Ts.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_SGouo838Ts.log:	Updated the status of the job to grey and starting the next job
tmp_SGouo838Ts.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/3/tmp_ildndCIquW.pickle assemblaScripts.bin.pipeline.MakeLinkageStats with exit status 0
tmp_SGouo838Ts.log:	Passed the job, okay
tmp_SGouo838Ts.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/4/tmp_vJbf8kEflb.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_SGouo838Ts.log:	Making a stub follow on job
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR/localTempDir/*
tmp_SGouo838Ts.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_SGouo838Ts.log:	Updated the status of the job to grey and starting the next job
tmp_SGouo838Ts.log:	Traceback (most recent call last):
tmp_SGouo838Ts.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 71, in
tmp_SGouo838Ts.log:	samples, complete, totalLength, totalContainment = getContainment(pathIntervals, parseBedFile(bedFile))
tmp_SGouo838Ts.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 8, in parseBedFile
tmp_SGouo838Ts.log:	intervals = [ fn(line.split()[:3]) for line in open(file, 'r').readlines() ]
tmp_SGouo838Ts.log:	IOError: [Errno 2] No such file or directory: '../../data/tests/little/beds/test1.bed'
tmp_SGouo838Ts.log:	Caught an exception in the target being run
tmp_SGouo838Ts.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_uk852TH2R4/4/tmp_vJbf8kEflb.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals with exit status 1
tmp_SGouo838Ts.log:	Failed the job
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR/localTempDir/*
tmp_SGouo838Ts.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_SGouo838Ts.log:	Exiting the slave because of a failed job
tmp_SGouo838Ts.log:	Running the command: mv /tmp/tmpdPL6kR/temp.log /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_f4KjSp3MBS.log
tmp_SGouo838Ts.log:	Written out an updated job file
tmp_SGouo838Ts.log:	Finished running the chain of jobs on this node, we ran for a total of 0.064972 seconds
tmp_SGouo838Ts.log:	Running the command: rm -rf /tmp/tmpdPL6kR
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_DE96HHppxf.xml is completely failed
Going to load the file /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml failed
The log file of the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_P9bPfHNPoh.log
tmp_P9bPfHNPoh.log:	Loading the class name assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_P9bPfHNPoh.log:	Setup logging with level: DEBUG
tmp_P9bPfHNPoh.log:	Running the command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed
tmp_P9bPfHNPoh.log:	Traceback (most recent call last):
tmp_P9bPfHNPoh.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/bin/jobTreeSlave", line 119, in processJob
tmp_P9bPfHNPoh.log:	jobTree.scriptTree.scriptTree.run(tempJob, l[1], l[2:])
tmp_P9bPfHNPoh.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/scriptTree.py", line 42, in run
tmp_P9bPfHNPoh.log:	target.execute(job)
tmp_P9bPfHNPoh.log:	File "/home/ravinkazo/ASSEMBLATHON/jobTree/scriptTree/stack.py", line 218, in execute
tmp_P9bPfHNPoh.log:	target.run()
tmp_P9bPfHNPoh.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/pipeline.py", line 236, in run
tmp_P9bPfHNPoh.log:	system("python %s/bedFileIntersection.py %s %s %s" % (binPath, contigPathOutputFile, contigPathOverlapFile, self.options.featureBedFiles))
tmp_P9bPfHNPoh.log:	File "/home/ravinkazo/ASSEMBLATHON/sonLib/bioio.py", line 158, in system
tmp_P9bPfHNPoh.log:	raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
tmp_P9bPfHNPoh.log:	RuntimeError: Command: python /home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/splitContigPaths.bed ../../output/tests/little/Escherichia_coliO83_H1_1.fa.complete/contigPathsFeatureOverlap.xml ../../data/tests/little/beds/test1.bed ../../data/tests/little/beds/test2.bed exited with non-zero status 1
The log file of the slave for the job
Reporting file: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/slaveLogFileDir/tmp_bn8Z25FyXg/tmp_DMe2lTBq6r/tmp_8YDOhOjeq9/tmp_iQVZulCup6.log
tmp_iQVZulCup6.log:	Parsed arguments and set up logging
tmp_iQVZulCup6.log:	Loaded the environment for the process
tmp_iQVZulCup6.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_qaL5TWf44I/4/tmp_w7Zc4KIPxP.pickle assemblaScripts.bin.pipeline.MakeCoveragePlots with exit status 0
tmp_iQVZulCup6.log:	Passed the job, okay
tmp_iQVZulCup6.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/1/tmp_0bUBTVFHpo.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats
tmp_iQVZulCup6.log:	Making a stub follow on job
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3/localTempDir/*
tmp_iQVZulCup6.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_iQVZulCup6.log:	Updated the status of the job to grey and starting the next job
tmp_iQVZulCup6.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/1/tmp_0bUBTVFHpo.pickle assemblaScripts.bin.pipeline.MakeSubstitutionStats with exit status 0
tmp_iQVZulCup6.log:	Passed the job, okay
tmp_iQVZulCup6.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/2/tmp_Od1No9XgtY.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats
tmp_iQVZulCup6.log:	Making a stub follow on job
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3/localTempDir/*
tmp_iQVZulCup6.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_iQVZulCup6.log:	Updated the status of the job to grey and starting the next job
tmp_iQVZulCup6.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/2/tmp_Od1No9XgtY.pickle assemblaScripts.bin.pipeline.MakeCopyNumberStats with exit status 0
tmp_iQVZulCup6.log:	Passed the job, okay
tmp_iQVZulCup6.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/3/tmp_8yHFgNS1GU.pickle assemblaScripts.bin.pipeline.MakeLinkageStats
tmp_iQVZulCup6.log:	Making a stub follow on job
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3/localTempDir/*
tmp_iQVZulCup6.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_iQVZulCup6.log:	Updated the status of the job to grey and starting the next job
tmp_iQVZulCup6.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/3/tmp_8yHFgNS1GU.pickle assemblaScripts.bin.pipeline.MakeLinkageStats with exit status 0
tmp_iQVZulCup6.log:	Passed the job, okay
tmp_iQVZulCup6.log:	Making a child with command: scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/4/tmp_3KD1fCX82S.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals
tmp_iQVZulCup6.log:	Making a stub follow on job
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3/localTempDir/*
tmp_iQVZulCup6.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_iQVZulCup6.log:	Updated the status of the job to grey and starting the next job
tmp_iQVZulCup6.log:	Traceback (most recent call last):
tmp_iQVZulCup6.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 71, in
tmp_iQVZulCup6.log:	samples, complete, totalLength, totalContainment = getContainment(pathIntervals, parseBedFile(bedFile))
tmp_iQVZulCup6.log:	File "/home/ravinkazo/ASSEMBLATHON/assemblaScripts/bin/bedFileIntersection.py", line 8, in parseBedFile
tmp_iQVZulCup6.log:	intervals = [ fn(line.split()[:3]) for line in open(file, 'r').readlines() ]
tmp_iQVZulCup6.log:	IOError: [Errno 2] No such file or directory: '../../data/tests/little/beds/test1.bed'
tmp_iQVZulCup6.log:	Caught an exception in the target being run
tmp_iQVZulCup6.log:	Ran the job command=scriptTree /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/tempDirDir/tmp_9dApxRpRFX/tmp_BSLMJFS2ZN/tmp_sqqxomu2Xe/tmp_HlxMOJig7F/4/tmp_3KD1fCX82S.pickle assemblaScripts.bin.pipeline.MakeContigAndScaffoldPathIntervals with exit status 1
tmp_iQVZulCup6.log:	Failed the job
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3/localTempDir/*
tmp_iQVZulCup6.log:	Cleaned up by removing the contents of the local temporary file directory for the job
tmp_iQVZulCup6.log:	Exiting the slave because of a failed job
tmp_iQVZulCup6.log:	Running the command: mv /tmp/tmplhlHk3/temp.log /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/logFileDir/tmp_mNBpMYb00p/tmp_Rbc0VkKEYm/tmp_4BxI3IRnLY/tmp_P9bPfHNPoh.log
tmp_iQVZulCup6.log:	Written out an updated job file
tmp_iQVZulCup6.log:	Finished running the chain of jobs on this node, we ran for a total of 0.062841 seconds
tmp_iQVZulCup6.log:	Running the command: rm -rf /tmp/tmplhlHk3
Job: /home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little/jobTree/jobs/tmp_esO5ZkdNd3/tmp_dIGVy8rkAa/tmp_q6mi1SrJ7S/tmp_iX2husNE3C.xml is completely failed
Only failed jobs and their dependents (4 total) are remaining, so exiting.
Finished the main loop
Done with job tree
jobTreeStatus --jobTree ./jobTree --failIfNotComplete
There are 4 jobs currently in job tree: ./jobTree
Colour: blue, number of jobs: 1
Colour: red, number of jobs: 3
make[1]: *** [pipeline] Error 1
make[1]: Leaving directory `/home/ravinkazo/ASSEMBLATHON/assemblaScripts/tests/little'
make: *** [testLittle] Error 2