ifiddes
commented
9 years ago What version of R are you using?
Also, if it still exists on your system, what does the file
/tmp/tmpbeZ6rc/localTempDir/fake_readtype_kmer_counts.txt
Contain?
Thanks,
Ian Fiddes
On Friday, April 17, 2015, twaddlac notifications@github.com wrote:
Good day,
I am receiving an error when running 'make test.' I have all of the dependencies and it seems as though all the submodules compiled successfully.
Here's the info that I deem relevant to debugging from the testLog.txt output. Let me know if you need the rest of the file:
The job seems to have left a log file, indicating failure: /opt/bioinformatics-software/minion-software/nanopore/testJobTree/jobs/t0/t0/job Reporting file: /opt/bioinformatics-software/minion-software/nanopore/testJobTree/jobs/t0/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Parsed arguments and set up logging log.txt: Error in sample.int(x, size, replace, prob) : log.txt: too few positive probabilities log.txt: Calls: replicate ... trial_fn -> matrix -> table -> factor -> sample -> sample.int log.txt: Execution halted log.txt: Traceback (most recent call last): log.txt: File "/opt/bioinformatics-software/minion-software/nanopore/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/opt/bioinformatics-software/minion-software/nanopore/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/opt/bioinformatics-software/minion-software/nanopore/nanopore/metaAnalyses/unmappedKmerAnalysis.py", line 51, in run log.txt: system("Rscript nanopore/metaAnalyses/mappable_kmer_analysis.R {} {} {} {}".format(os.path.join(self.getLocalTempDir(), readType + "_kmer_counts.txt"), os.path.join(self.outputDir, readType + "_unmapped_kmer_counts.txt"), os.path.join(self.outputDir, readType + "_unmapped_top_bot_sigkmer_counts.txt"), os.path.join(self.outputDir, readType + "_volcano_plot.pdf"))) log.txt: File "/opt/bioinformatics-software/minion-software/nanopore/submodules/sonLib/bioio.py", line 184, in system log.txt: raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) log.txt: RuntimeError: Command: Rscript nanopore/metaAnalyses/mappable_kmer_analysis.R /tmp/tmpbeZ6rc/localTempDir/fake_readtype_kmer_counts.txt tests/output/metaAnalysis_UnmappedKmerAnalysis/fake_readtype_unmapped_kmer_counts.txt tests/output/metaAnalysis_UnmappedKmerAnalysis/fake_readtype_unmapped_top_bot_sigkmer_counts.txt tests/output/metaAnalysis_UnmappedKmerAnalysis/fake_readtype_volcano_plot.pdf exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host zoidberg log.txt: Due to failure we are reducing the remaining retry count of job /opt/bioinformatics-software/minion-software/nanopore/testJobTree/jobs/t0/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /opt/bioinformatics-software/minion-software/nanopore/testJobTree/jobs/t0/t0/job is completely failed Only failed jobs and their dependents (1 total) are remaining, so exiting. Finished the main loop Waiting for stats collator process to finish Stats finished collating in 0.346755981445 seconds Traceback (most recent call last): File "./nanopore/pipeline.py", line 214, in
main() File "/opt/bioinformatics-software/minion-software/nanopore/nanopore/pipeline.py", line 210, in main raise RuntimeError("Got failed jobs") RuntimeError: Got failed jobs — Reply to this email directly or view it on GitHub https://github.com/mitenjain/nanopore/issues/7.
Ian Fiddes
twaddlac
Good day,
I am receiving an error when running 'make test.' I have all of the dependencies and it seems as though all the submodules compiled successfully.
Here's the info that I deem relevant to debugging from the testLog.txt output. Let me know if you need the rest of the file: