Deeptool ComputeGCBias causes fatal error
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5.6 years ago
mfro1505 • 0

Hi together!
I tried to use the deeptool ComputeGCBias with a sorted BAM file as Input. I used a BAM file directly from BWA mapping, a filtered BAM file (SAM tools, Filter SAM or BAM), and an additionally sorted BAM file. I always get the same error code that I cannot explain.

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/usr/local/tools/_conda/envs/mulled-v1-4b8f57f006cc92d851cc49218dae7aad45ffa09ba66fc274bc342ee27143a74c/bin/computeGCBias", line 11, in <module>
    main(args)
  File "/usr/local/tools/_conda/envs/mulled-v1-4b8f57f006cc92d851cc49218dae7aad45ffa09ba66fc274bc342ee27143a74c/lib/python3.6/site-packages/deeptools/computeGCBias.py", line 657, in main
    tbit = py2bit.open(global_vars['2bit'])
RuntimeError: Received an error during file opening!

I appreciate your help so much, thank you!
Best!

deeptools computegcbias software error sequencing • 1.9k views
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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

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Tagging: Devon Ryan

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Please show the full command lines.

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ln -s '/data/dnb02/galaxy_db/files/008/052/dataset_8052960.dat' local_bamInput.bam && 
ln -s '/data/dnb02/galaxy_db/files/_metadata_files/000/144/metadata_144274.dat' local_bamInput.bam.bai &&  
computeGCBias --numberOfProcessors "${GALAXY_SLOTS:-4}" --bamfile local_bamInput.bam
--GCbiasFrequenciesFile /data/dnb02/galaxy_db/files/008/053/dataset_8053017.dat    
--genome  '/data/db/data_managers/mm10/seq/mm10.2bit,/data/db/reference_genomes/mm10/seq/mm10.2bit'  
--effectiveGenomeSize 2308125349  
--biasPlot /data/dnb02/galaxy_db/files/008/053/dataset_8053018.dat 
--plotFileFormat png
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Try putting only one .2bit file here. (And you typed two spaces between genome and '/data... here. Idk if it's wrong in command)

--genome  '/data/db/data_managers/mm10/seq/mm10.2bit,/data/db/reference_genomes/mm10/seq/mm10.2bit'

Like this line:

--genome /data/db/data_managers/mm10/seq/mm10.2bit
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Where'd you get the 2bit file?

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having the same issue here. I made the 2bit file by using the UCSC tool faToTwoBit with the GRCH38 genoma.fa file from illumina iGenomes

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Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate. I've moved your post to a comment this time.

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