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License: MIT License
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Dependancies issue
Hi!
I tried to compile nanpore and found 2 minor issues:
1 the git submodules use ssh connection to github can not be publicly accessed.
if you change them to HTTPS then they could be cloned:
[submodule "submodules"]
path = submodules
url = https://github.com/benedictpaten/jobTree.git
[submodule "subModules/jobTree"]
path = subModules/jobTree
url = https://github.com/benedictpaten/jobTree.git
[submodule "subModules/sonLib"]
path = subModules/sonLib
url = https://github.com/benedictpaten/sonLib.git
[submodule "submodules/bwa"]
path = submodules/bwa
url = https://github.com/lh3/bwa.git
[submodule "submodules/lastz"]
path = submodules/lastz
url = https://github.com/UCSCReconGroup/lastz.git
[submodule "submodules/jobTree"]
path = submodules/jobTree
url = https://github.com/benedictpaten/jobTree.git
[submodule "submodules/sonLib"]
path = submodules/sonLib
url = https://github.com/benedictpaten/sonLib.git
[submodule "submodules/last"]
path = submodules/last
url = https://github.com/UCSCReconGroup/last.git
[submodule "submodules/blasr"]
path = submodules/blasr
url = https://github.com/PacificBiosciences/blasr.git
[submodule "submodules/hdf5"]
path = submodules/hdf5
url = https://github.com/UCSCReconGroup/hdf5.git
[submodule "submodules/cactus"]
path = submodules/cactus
url = https://github.com/benedictpaten/cactus.git
2 Building nanopore (or one of its dependancies) requires the Tokyocabinet library.
On Ubuntu this can be solved with sudu apt-get install libtokyocabinet-dev
Thanks!
kind regards,
Sophie
bwa mem
Why is bwa-mem used with the pacbio option instead of the ont2d?
Error when performing 'make test'
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 <module>
main()
File "/opt/bioinformatics-software/minion-software/nanopore/nanopore/pipeline.py", line 210, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs
compilation issue
I got this error when compiling:
In file included from impl/cactusBlock.c:7:0:
impl/cactusGlobalsPrivate.h:22:20: fatal error: tcutil.h: No such file or directory
compilation terminated.
Error when performing "make test"
Hello.
I got this error.
Link to testLog.txt: click
$ make test
[...]
./nanopore/pipeline.sh tests testJobTree testLog.txt 4 singleMachine 8589934592
make: *** [test] Error 1
Got message from job at time: 1509127924.78 : Hmm with highest likelihood: -2431613448.59
Got message from job at time: 1509127931.15 : Starting analysis Hmm for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis GlobalCoverage for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis LocalCoverage for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis Substitutions for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis Indels for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis AlignmentUncertainty for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis ChannelMappability for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis KmerAnalysis for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Got message from job at time: 1509127931.15 : Starting analysis IndelKmerAnalysis for reference file tests/output/processedReferenceFastaFiles/reference.fa and read file tests/output/processedReadFastqFiles/fake_readtype/reads.fq analyzed with mapper LastzParamsRealignEm
Only failed jobs and their dependents (4 total) are remaining, so exiting.
Finished the main loop
Waiting for stats collator process to finish
Stats finished collating in 0.479724168777 seconds
Traceback (most recent call last):
File "./nanopore/pipeline.py", line 214, in <module>
main()
File "/ibers/ernie/home/eac16/local/nanopore/nanopore/pipeline.py", line 210, in main
raise RuntimeError("Got failed jobs")
RuntimeError: Got failed jobs
Can you help me?
My best regards.
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