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lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
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problem with "seqcluster report" command #20

Closed AlexandraBomane closed 8 years ago

AlexandraBomane commented 8 years ago

Hello lpantano,

I had the following error launching the command "seqcluster report -j seqcluster.json -o Report -r ref.fasta" :

................. INFO locus bigger > 500 nt, skipping: [[1108, u'1', 207324614, 207326831, u'+', 35]] INFO locus bigger > 500 nt, skipping: [[3617, u'11', 62882013, 62882997, u'+', 11]] INFO locus bigger > 500 nt, skipping: [[7088, u'15', 40038287, 40038885, u'-', 19]] INFO locus bigger > 500 nt, skipping: [[16701, u'6', 26538052, 26687281, u'+', 659]] ['report', '-j', 'ClusteringStep/seqcluster.json', '-o', 'ReportStep', '-r', '/root/Homo_sapiens.GRCh38.dna.toplevel.cleaned.fasta'] Traceback (most recent call last): File "/usr/local/bin/seqcluster", line 9, in load_entry_point('seqcluster==1.2.3a0', 'console_scripts', 'seqcluster')() File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 31, in main report(kwargs["args"]) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/create_report.py", line 32, in report data = make_profile(data, out_dir, args) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/libs/report.py", line 66, in make_profile data[0][c]['precursor'].update(run_rnafold(data[0][c]['precursor']['seq'])) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/function/rnafold.py", line 12, in run_rnafold process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 7] Argument list too long

I don't understand how this error was triggered. How can I avoid this problem ?

Thanks, Alexandra

lpantano commented 8 years ago

Hi,

I just pushed a fix for that, hoping is that. Can you update to development? There should be a command seqcluster_install --upgrade that should install from github.

Let me know if that works.

AlexandraBomane commented 8 years ago

Hi,

I tested your modification and it works very well ! :)

I pushed a Docker image of bcbio-nextgen to propose a working version of seqcluster including this last modification (alexandrabomane/bcbio-nextgen). I hope it doesn't bother you.

Thanks, Alexandra