search

PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
Other
204 stars 103 forks source link

quiver-run failed at variantCaller #712

Closed yanboANU closed 3 years ago

yanboANU commented 3 years ago

Dear FALCON developers,

When I use FALCON and FALCON-unzip, I have an issue with the last step of the workflow, fc_quiver.py.

It reports: [ERROR]Task Node(4-quiver/cns-output) failed with exit-code=1 [ERROR]Some tasks are recently_done but not satisfied: set([Node(4-quiver/cns-output)])

After I traceback, I found some folders in quiver-run seem work and others fail. du -sh 4-quiver/quiver-run//uow-00/fa*

0 4-quiver/quiver-run/000000Fp01_00001/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00001/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01_00002/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00002/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01_00003/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00003/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01_00004/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00004/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01_00005/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00005/uow-00/cns.fastq.gz 8.0K 4-quiver/quiver-run/000000Fp01_00006/uow-00/cns.fasta.gz 12K 4-quiver/quiver-run/000000Fp01_00006/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01_00007/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01_00007/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000000Fp01/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000000Fp01/uow-00/cns.fastq.gz 0 4-quiver/quiver-run/000001Fp01_00001/uow-00/cns.fasta.gz 0 4-quiver/quiver-run/000001Fp01_00001/uow-00/cns.fastq.gz 12K 4-quiver/quiver-run/000001Fp01_00002/uow-00/cns.fasta.gz 12K 4-quiver/quiver-run/000001Fp01_00002/uow-00/cns.fastq.gz 12K 4-quiver/quiver-run/000001Fp01_00003/uow-00/cns.fasta.gz 12K 4-quiver/quiver-run/000001Fp01_00003/uow-00/cns.fastq.gz ...

In the failed cases, I found variantCaller is the reason.

In 4-quiver/quiver-run/000000Fp01 run-P074fdf05ba6afa.bash.stderr: ... variantCaller --algorithm=arrow -x 5 -X 120 -q 20 -j 24 -r /path/4-quiver/quiver-split/./refs/000000Fp01/ref.fa aln-000000Fp01.bam -o cns.fasta.gz -o cns.fastq.gz --minConfidence 0 -o cns.vcf Process ArrowWorkerProcess-6: Traceback (most recent call last): File "/miniconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/Worker.py", line 67, in run self._run() File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/Worker.py", line 48, in _run result = self.onChunk(datum) File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/arrow/arrow.py", line 164, in onChunk refContig, options.coverage, self.arrowConfig) File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/arrow/arrow.py", line 90, in consensusAndVariantsForWindow alnsUsed=alnsUsed) File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/arrow/utils.py", line 462, in consensusForAlignments mappedReads = [ arrowConfig.extractMappedRead(aln, refStart) for aln in alns ] File "/miniconda2/lib/python2.7/site-packages/GenomicConsensus-2.2.2-py2.7.egg/GenomicConsensus/arrow/model.py", line 83, in extractMappedRead aln.read(aligned=False, orientation="native"), File "/miniconda2/lib/python2.7/site-packages/pbcore/io/align/BamAlignment.py", line 540, in read ungapped = reverseComplementAscii(clipped) if shouldReverse else clipped File "/miniconda2/lib/python2.7/site-packages/pbcore/io/align/_BamSupport.py", line 39, in reverseComplementAscii return complementAscii(a)[::-1] File "/miniconda2/lib/python2.7/site-packages/numpy/lib/function_base.py", line 1972, in call return self._vectorize_call(func=func, args=vargs) File "/miniconda2/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2051, in _vectorize_call res = array(outputs, copy=False, subok=True, dtype=otypes[0]) TypeError: long() argument must be a string or a number, not 'NoneType' Process ArrowWorkerProcess-1: ...

I use --log-level DEBUG: variantCaller --algorithm=arrow -x 5 -X 120 -q 20 -j 24 -r /path/4-quiver/quiver-split/./refs/000000Fp01/ref.fa aln-000000Fp01.bam -o cns.fasta.gz -o cns.fastq.gz --minConfidence 0 -o cns.vcf --log-level DEBUG

[DEBUG] ArrowWorkerProcess-3 received work unit, coords=000000Fp01:12000-12500 [INFO] Arrow operating on 000000Fp01:11995-12505 [ERROR] Child process exited with exitcode=1. Aborting. [DEBUG] ArrowWorkerProcess-5 received work unit, coords=000000Fp01:12500-13000 [INFO] Arrow operating on 000000Fp01:12495-13005 [ERROR] Aborting [INFO] exiting with return code -1 in 2.82 sec.

Could anyone please tell me where I am going wrong? It's weird to me some folders in quiver-run work and some not.

pb-cdunn commented 3 years ago

It's very difficult to continue to support FALCON, for a variety of reasons. We highly recommend adopting CCS reads and switching to pbipa in Bioconda.