Question: Error with correctGCBias in deepTools
0
gravatar for clmin
2.7 years ago by
clmin10
clmin10 wrote:

Hello,

I'm trying to correct the GC bias with deepTools. I successfully used computeGCBias

computeGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit -l 200 --GCbiasFrequenciesFile freq.txt -v

But the next step, correctGCBias, return an error I don't understand.

correctGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit --GCbiasFrequenciesFile freq.txt -o gc_file.bam -v

applying correction

genome partition size for multiprocessing: 56882182

using region None

({'chrY': 'chrY', 'chrX': 'chrX', 'chr13': 'chr13', 'chr12': 'chr12', 'chr11': 'chr11', 'chr10': 'chr10', 'chr17': 'chr17', 'chr16': 'chr16', 'chr15': 'chr15', 'chr14': 'chr14', 'chr19': 'chr19', 'chr18': 'chr18', 'chrM': 'chrM', 'chr7': 'chr7', 'chr6': 'chr6', 'chr5': 'chr5', 'chr4': 'chr4', 'chr3': 'chr3', 'chr2': 'chr2', 'chr1': 'chr1', 'chr9': 'chr9', 'chr8': 'chr8'}, {'chrY': 'chrY', 'chrX': 'chrX', 'chr13': 'chr13', 'chr12': 'chr12', 'chr11': 'chr11', 'chr10': 'chr10', 'chr17': 'chr17', 'chr16': 'chr16', 'chr15': 'chr15', 'chr14': 'chr14', 'chr19': 'chr19', 'chr18': 'chr18', 'chrM': 'chrM', 'chr7': 'chr7', 'chr6': 'chr6', 'chr5': 'chr5', 'chr4': 'chr4', 'chr3': 'chr3', 'chr2': 'chr2', 'chr1': 'chr1', 'chr9': 'chr9', 'chr8': 'chr8'})

using 4 processors for 59 number of tasks

Sam for chr10 0 56882182

Sam for chr11 56882182 113764364

Sam for chr12 113764364 121257530

Sam for chr14 0 56882182

Sam for chr15 56882182 103494974

Traceback (most recent call last):

File "/usr/local/bin/correctGCBias", line 11, in <module>

main(args)

File "/usr/local/lib/python2.7/dist-packages/deeptools/correctGCBias.py", line 628, in main

writeCorrectedSam_wrapper, mp_args).get(9999999)

File "/usr/lib/python2.7/multiprocessing/pool.py", line 567, in get

raise self._value

ValueError: invalid value type 'B' (<type 'str'="">)

Could anyone help me?

bam next-gen deeptools • 849 views
ADD COMMENTlink modified 2.7 years ago by Devon Ryan92k • written 2.7 years ago by clmin10
1

I think that's all newest version:

deeptools 2.4.2-4-999ec5d

pysam==0.10.0

ADD REPLYlink written 2.7 years ago by clmin10

OK, please run this with one thread then and post the resulting error message. To properly fix this I might need a copy of the relevant portion of the BAM file (at least the region with the first alignment that's causing this behavior).

ADD REPLYlink written 2.7 years ago by Devon Ryan92k

My guess is that this is an issue with the version of pysam that you're using. Can you post the following:

  1. The version of deepTools you have installed
  2. The version of pysam you have installed (pip freeze | grep pysam may tell you this).

I know it's a pain, but it might also help to run this single threaded. The error messages are more informative then.

ADD REPLYlink written 2.7 years ago by Devon Ryan92k

I'm not sure I understand, my first post was one thread and the resulting error message. For the relevant part of the bam, I don't know what that it, sorry.

ADD REPLYlink written 2.7 years ago by clmin10

You were using 4 threads, even though you didn't specify it (it wasn't my idea, but deepTools will use 1/2 of the cores on a server unless you tell it explicitly how many it should use). Just rerun it with -p 1.

ADD REPLYlink written 2.7 years ago by Devon Ryan92k

It seems the same:

correctGCBias -b ctr1.bam --effectiveGenomeSize 2150570000 -g mm9.2bit --GCbiasFrequenciesFile ct1_j28.txt -o gc_ct1_j28.bam -p 1 -v

applying correction

genome partition size for multiprocessing: 23672257

using region None

({'chrY': 'chrY', 'chrX': 'chrX', 'chr13': 'chr13', 'chr12': 'chr12', 'chr11': 'chr11', 'chr10': 'chr10', 'chr17': 'chr17', 'chr16': 'chr16', 'chr15': 'chr15', 'chr14': 'chr14', 'chr19': 'chr19', 'chr18': 'chr18', 'chrM': 'chrM', 'chr7': 'chr7', 'chr6': 'chr6', 'chr5': 'chr5', 'chr4': 'chr4', 'chr3': 'chr3', 'chr2': 'chr2', 'chr1': 'chr1', 'chr9': 'chr9', 'chr8': 'chr8'}, {'chrY': 'chrY', 'chrX': 'chrX', 'chr13': 'chr13', 'chr12': 'chr12', 'chr11': 'chr11', 'chr10': 'chr10', 'chr17': 'chr17', 'chr16': 'chr16', 'chr15': 'chr15', 'chr14': 'chr14', 'chr19': 'chr19', 'chr18': 'chr18', 'chrM': 'chrM', 'chr7': 'chr7', 'chr6': 'chr6', 'chr5': 'chr5', 'chr4': 'chr4', 'chr3': 'chr3', 'chr2': 'chr2', 'chr1': 'chr1', 'chr9': 'chr9', 'chr8': 'chr8'})

Sam for chr10 0 23672257

Traceback (most recent call last):

File "/usr/local/bin/correctGCBias", line 11, in <module>

main(args)

File "/usr/local/lib/python2.7/dist-packages/deeptools/correctGCBias.py", line 630, in main

res = list(map(writeCorrectedSam_wrapper, mp_args))

File "/usr/local/lib/python2.7/dist-packages/deeptools/correctGCBias.py", line 286, in writeCorrectedSam_wrapper

return writeCorrectedSam_worker(*args)

File "/usr/local/lib/python2.7/dist-packages/deeptools/correctGCBias.py", line 413, in writeCorrectedSam_worker

read.set_tags(readTag)

File "pysam/libcalignedsegment.pyx", line 2113, in pysam.libcalignedsegment.AlignedSegment.set_tags >

(pysam/libcalignedsegment.c:23066)

File "pysam/libcalignedsegment.pyx", line 295, in pysam.libcalignedsegment.packTags >

(pysam/libcalignedsegment.c:6217)

ValueError: invalid value type 'B' (<type 'str'="">)

ADD REPLYlink written 2.7 years ago by clmin10

OK, it's in the set_tags() function, which is the part I needed to know. Can you extract chr10:1-23672257 into a BAM file and post that and your freq.txt file somewhere? Then I can figure out a patch.

ADD REPLYlink written 2.7 years ago by Devon Ryan92k

BAM file: https://e-nautia.com/share/45076-x8zr2q6p

Freqence file: https://e-nautia.com/share/45077-yzmr244h

ADD REPLYlink written 2.7 years ago by clmin10

Thanks, this turns out to be a bug in pysam. I'm trying to find out now if an earlier version handled this correctly. Whatever aligner you're using producing auxiliary tags that pysam is having problems with.

ADD REPLYlink written 2.7 years ago by Devon Ryan92k
0
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

I've posted a bug report to pysam. You can follow the progress of it here.

ADD COMMENTlink written 2.7 years ago by Devon Ryan92k
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