sre_constants.error: nothing to repeat

[me.x...@gmail.com]

My dataset is a mouse RNA-Seq with pair-end, I ran the following command

trust -f 4021.9515.1068493.P100.W101104.bam -g mm10 -n 6

And trust switched to single-end automatically due to short insert size. However, I got the following error message, any possible reasons? Could it be related to python version. I have python2.7+trust3.0.02. Thanks.

('Read length:', 100)

ScreenGenome Finished! sr =  1

Total reads extracted 121846

Informative read pairs kept 8440

Switching to single end mode

# Extract reads with joining gene DNA motif

1000000

2000000

3000000

53

Traceback (most recent call last):

  File "/home/yh/anaconda/envs/bio.pipe/bin/trust", line 4, in <module>

    __import__('pkg_resources').run_script('trust==3.0.2', 'trust')

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script

    exec(code, namespace, namespace)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/trust", line 18, in <module>

    main()

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/trust", line 14, in main

    trust_main(opt)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/trust/trust_main.py", line 261, in trust_main

    annList,ContigFinalList=ProcessSingleEndReads(ff,LocusFile,HeavyChain=HC,light_chain=light_chain,err=Err,overlap_thr=thr_L,fasta=fasta,Bcell=Bcell, genome=ReferenceGenome)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/trust/single_end_mode.py", line 345, in ProcessSingleEndReads

    pat=re.compile(pp)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/re.py", line 194, in compile

    return _compile(pattern, flags)

  File "/home/yh/anaconda/envs/bio.pipe/lib/python2.7/re.py", line 251, in _compile

    raise error, v # invalid expression

sre_constants.error: nothing to repeat

[Bo Li]

It seems to be a re.compile error, which I have never seen before. Can you see if this command works in your python console:

pat=re.compile('CA.S')

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[me.x...@gmail.com]

Bo, the command works well. By the way, it seems a previous thread also report the same error, also for mm10. Maybe something related to mouse sequence? 

[rnaseq.pipeline@shepard ~]$ source activate bio.pipe

(bio.pipe) [rnaseq.pipeline@shepard ~]$ python

Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

Anaconda is brought to you by Continuum Analytics.

Please check out: http://continuum.io/thanks and https://anaconda.org

>>> import re

>>> pat=re.compile('CA.S')

>>> pat

<_sre.SRE_Pattern object at 0x2aaaab2c9c00>

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[Bo Li]

Interesting.

Jian, could you please help with this when you have time? I am not sure why mm10 is different from human.

Thanks,

Bo

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[jian zhang]

Hi,

Thank you for reporting the issue, I guess this was because the stop codon (‘*’) in some mouse VJ AA sequences. I have fixed this bug, please try the new release (v3.0.3) of TRUST on the Bitbucket and let me know if there are any other problems.

Thanks,

Jian

[Bo Li]

Thanks Jian for the updates!

Best,

Bo

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[Ying Huang]

Jian, it works well after upgraded to v3.0.3. Thanks for all your help. Ying