Closed mmaslon closed 4 months ago
Could you try creating a tab-separated file and naming it with *.tsv
suffix and rerun it instead of the files_test.txt
file?
I am still getting an error, though a different one:
the command is:
files="/bla/files_test.tsv" slamdunk all -r $reference -b $bed -o $output_dir -5 12 -n 100 -m -mv 0.2 -rl 85 --skip-sam $files
the files_test.tsv is:
/bla/slurm_jobdir/slamseq_data/trimmed_reads/Unknown_A1BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq.gz rep1 LKO 0
slamdunk all Running slamDunk map for 1 files (1 threads) . Running slamDunk filter for 1 files (1 threads) Traceback (most recent call last): File "/bla.conda/envs/slamdunk/bin/slamdunk", line 10, in
sys.exit(run()) ^^^^^ File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/slamdunk/slamdunk.py", line 520, in run runAll(args) File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/slamdunk/slamdunk.py", line 274, in runAll results = Parallel(n_jobs=n, verbose=verbose)(delayed(runFilter)(tid, dunkbufferIn[tid], bed, args.mq, args.identity, args.nm, dunkPath) for tid in range(0, len(samples))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/joblib/parallel.py", line 1918, in call return output if self.return_generator else list(output) ^^^^^^^^^^^^ File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/joblib/parallel.py", line 1847, in _get_sequential_output res = func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/slamdunk/slamdunk.py", line 170, in runFilter filter.Filter(bam, outputBAM, getLogFile(outputLOG), bed, mq, minIdentity, maxNM, printOnly, verbose) File "/bla/.conda/envs/slamdunk/lib/python3.12/site-packages/slamdunk/dunks/filter.py", line 225, in Filter infile = pysam.AlignmentFile(inputBAM, "rb") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 961, in pysam.libcalignmentfile.AlignmentFile._open File "pysam/libchtslib.pyx", line 361, in pysam.libchtslib.HTSFile.check_truncation OSError: no BGZF EOF marker; file may be truncated
Are you sure you have enough memory / storage space? That reads somehow like the files is corrupt and writing to it was prematurely aborted
Thank you for your quick response. I tested the script one by one (i.e. map, snp etc.), and it turns out that counting step does not "like" fa.gz as a reference - needs to be gzipped or bgzipped. This sorted my issue.
Thank you for your help.
Magda
Hi there,
I am trying to execute slamdunk with samplesheet, and I am running into a problem - the reads are not used correctly as an input.
If I run the pipeline with the name of the file it works fine:
slamdunk all -r $reference -b $bed -o $output_dir -5 12 -n 100 -m -mv 0.2 -rl 85 --skip-sam /bla/slurm_jobdir/slamseq_data/trimmed_reads/Unknown_A1BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq.gz
however if I try to use the samplesheet instead:
where
gdzie files_test.txt, to:
I get the following error:
Can I please ask what the issue might be?