Closed jonwruffin closed 3 years ago
To add to this, I get the same error when running alleyoop utrrates.
Hi,
looks like there's something wrong with the bed file - how does it look?
Fixed. The BED file had a header, removing it solves the problem.
I get the following error when running the count dunk (all previous dunks successfully completed):
(slammer2) jonwruffin@DESKTOP-DGJU5CE:/mnt/e/slamseq_run_9_9_2021$ slamdunk count -o /mnt/e/slamseq_run_9_9_2021/count -s /mnt/e/slamseq_run_9_9_2021/snp/ -r /mnt/e/slamseq_run_9_9_2021/hg19_no_alt_analysis_set.fa -b /mnt/e/slamseq_run_9_9_2021/pure_UTR_3_hg19_ensemble.bed /mnt/e/slamseq_run_9_9_2021/filter/*_slamdunk_mapped_filtered.bam
Running slamDunk tcount for 36 files (1 threads) Traceback (most recent call last): File "/home/jonwruffin/anaconda3/envs/slammer2/bin/slamdunk", line 10, in
sys.exit(run())
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/slamdunk/slamdunk.py", line 516, in run
results = Parallel(n_jobs=n, verbose=verbose)(delayed(runCount)(tid, args.bam[tid], args.ref, args.bed, args.maxLength, args.minQual, args.conversionThreshold, outputDirectory, snpDirectory, vcfFile) for tid in range(0, len(args.bam)))
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/parallel.py", line 1041, in call
if self.dispatch_one_batch(iterator):
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/parallel.py", line 859, in dispatch_one_batch
self._dispatch(tasks)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/parallel.py", line 777, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 208, in apply_async
result = ImmediateResult(func)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 572, in init
self.results = batch()
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/parallel.py", line 262, in call
return [func(*args, *kwargs)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/joblib/parallel.py", line 262, in
return [func( args, **kwargs)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/slamdunk/slamdunk.py", line 202, in runCount
tcounter.computeTconversions(ref, bed, inputSNP, bam, maxLength, minQual, outputCSV, outputBedgraphPlus, outputBedgraphMinus, conversionThreshold, log)
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/slamdunk/dunks/tcounter.py", line 165, in computeTconversions
for utr in BedIterator(bed):
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/slamdunk/utils/BedReader.py", line 81, in next
return self._toBED(self._bedFile.next())
File "/home/jonwruffin/anaconda3/envs/slammer2/lib/python3.9/site-packages/slamdunk/utils/BedReader.py", line 67, in _toBED
bedEntry.start = int(cols[1])
IndexError: list index out of range
I initially ran "slamdunk all" and it ran into this error on the count step, rerunning the count step separately produces the same error message. Any advice on how to proceed? Thanks in advance.