Question: Deeptool ComputeGCBias causes fatal error
0
gravatar for mfro1505
23 months ago by
mfro15050
mfro15050 wrote:

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!

ADD COMMENTlink modified 23 months ago by _r_am31k • written 23 months ago by mfro15050

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 23 months ago by _r_am31k

Tagging: Devon Ryan

ADD REPLYlink written 23 months ago by GenoMax92k

Please show the full command lines.

ADD REPLYlink written 23 months ago by ATpoint42k
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
ADD REPLYlink modified 23 months ago • written 23 months ago by mfro15050

Where'd you get the 2bit file?

ADD REPLYlink written 23 months ago by Devon Ryan97k
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