roryk
commented
6 years ago Thanks, sorry about that. That warning is innocuous and isn't the root cause of the problem. The steps that it is doing there is it is taking the cufflinks-assembly.gtf files for each sample, merging them together into a merged.gtf file and then cleaning up the final merged file into an assembly.gtf file. Are the cufflinks-assembly.gtf files floating around and do they look weird? What about the merged.gtf and assembly files?
aadamk
I get the following error post-star alignment and during cufflinks transcript assembly:
main(kwargs)
File "/home/aadam/local/bin/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 42, in run_main
fc_dir, run_info_yaml)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 86, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 243, in rnaseqpipeline
samples = rnaseq.assemble_transcripts(run_parallel, samples)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 285, in assemble_transcripts
samples = run_parallel("cufflinks_merge", [samples])
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"], batch_size=1)(joblib.delayed(fn)(x) for x in items):
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 804, in call
while self.dispatch_one_batch(iterator):
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 662, in dispatch_one_batch
self._dispatch(tasks)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 570, in _dispatch
job = ImmediateComputeBatch(batch)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 183, in init
self.results = batch()
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(*args, *kwargs) for func, args, kwargs in self.items]
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 50, in wrapper
return apply(f, args, *kwargs)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 387, in cufflinks_merge
return rnaseq.cufflinks_merge(args)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 246, in cufflinks_merge
samples[0][0])
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/cufflinks.py", line 259, in merge
filtered = annotate_gtf.cleanup_transcripts(classified, gtf_file, ref_file)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/annotate_gtf.py", line 52, in cleanup_transcripts
assembled_db = gtf.get_gtf_db(assembled_gtf)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py", line 43, in get_gtf_db
return gffutils.FeatureDB(db_file)
File "/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py", line 131, in init
version, dialect = c.fetchone()
TypeError: 'NoneType' object is not iterable
... 196662 genes finished Traceback (most recent call last): File "/home/aadam/local/bin/bcbio_nextgen.py", line 234, in
Not sure why there is an empty object - after completing the processing of ~19000 loci, the following warning appears in the middle of my log file: [2017-11-06T16:04Z] multiprocessing: cufflinks_merge /home/aadam/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py:85: UserWarning: 'infer_gene_extent' will be deprecated. For now, the following equivalent values were automatically set: 'disable_infer_genes=True', 'disable_infer_transcripts=True'. Please use these instead in the future. warnings.warn("'infer_gene_extent' will be deprecated. For now, "
After this, there are numerous messages stating 'x # of genes finished' after conversion of the .gtf to fasta format, then this error occurs. Not sure I understand it.