Problems with Pysam and deeptools [Help me, please..]

Question

[mink2mink2]

Hello, I'm setting up my PC to install pysam and deeptools.

1. Ubuntu 16.04LTS
2. pip install deeptools
3. #python
4. >>>import pysam
5. >>>print pysam.__version__
6. 0.9.1.4
7. >>>cn = pysam.view("-F4","-c",'./testbam.bam');
8. Segmentation fault ( core dumped )

this is an error. So I tried other way to install pysam.

1. pip uninstall pysam
2. apt-get install python-pysam
3. #python
4. >>>import pysam
5. >>> print pysam.__version__
6. 0.7.7
7. >>>cn = pysam.view("-F4","-c",'./testbam.bam');
8. >>>

I thought I solved but other error appear in deeptools

1. #computeGCBias --numberOfProcessors 16 --fragmentLength 160 --bamfile IonXpress_001_rawlib.bam --effectiveGenomeSize 2451960000 --genome /hprnd0001/hg19fa/hg19fa/hg19.2bit --GCbiasFrequenciesFile frequencies.txt --plotFileFormat png --biasPlot plot --regionSize 200
2. AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'get_tags'

So I back to install pysam again.

1. #pip install --upgrade pysam

then pysam version back to 0.9.1.4. And I did excute again "computeGCBias" command. and it is done well.

But first problem appeared again.(pysam's execution return "Segmentation Fault ( core dumped )"

my python version is 2.7.11. How can I solve this? Or is there a way to install pysam and deeptools well?

Please help me...

[Michael]

Help me please

is not a descriptive title, fixed.

Answer 1

[Devon Ryan]

deepTools requires pysam >= 0.8.2, which is why 0.7.7 is throwing an error. I have no clue why pysam is segfaulting, the easiest fix is to just use conda instead (you can conda install -c bioconda deeptools).

If for some reason you absolutely need to install with pip, then you can try an older version of pysam (e.g., pip install pysam==0.8.4).

[mink2mink2]

Thank you for your advice! I will try again with 0.8.4. BTW, newist deeptools is working good on ubuntu 16.04?

[Devon Ryan]

All versions of deepTools will work on any even remotely recent version of Linux.

[mink2mink2]

0.8.4 is working good. 0.7.7 is also working good. but 0.9.1.4 is not working. Please give me any idea..

[Michael]

did you check for the required version of the samtools or htseq library? Most tools use samtools instead of rolling their on BAM support.

[Devon Ryan]

pysam is using a bundled copy of htslib. Many people have had issues getting the various 0.9 releases of pysam installed, because of underlying changes in how htslib is itself compiled. I fully expect that the segfault is related to that.

[Devon Ryan]

For whatever reason pysam-0.9.1.4 isn't getting installed/compiled correctly on your system. Just don't use that version of pysam then.

Answer 2

[mink2mink2]

Thank you so much. I will check required version of the samtools and htseq lib. And I'm gonna use pysam-0.8.4 instead of 0.9.1.4. Thank you so much again!