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lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
35 stars 17 forks source link

Collapse #13

Closed filicado closed 8 years ago

filicado commented 8 years ago

I'm running seqcluster inside the provided docker container (https://hub.docker.com/r/bcbio/bcbio/)

When running the collapse script I encounter this error:

['collapse', '-f', '/seqdata/readscleaned/33_S1_body.fastq.clean', '-o', '/seqdata/collapsed'] INFO Run collapse Traceback (most recent call last): File "/usr/local/share/bcbio-nextgen/anaconda/bin/seqcluster", line 9, in load_entry_point('seqcluster==1.1.14', 'console_scripts', 'seqcluster')() File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/command_line.py", line 49, in main collapse_fastq(kwargs["args"]) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/collapse.py", line 13, in collapse_fastq seqs = collapse(args.fastq) File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/seqcluster/libs/fastq.py", line 11, in collapse with open_fastq(in_file) as handle: AttributeError: exit

Any ideas what the problem could be? Thanks

filicado commented 8 years ago

sorry stupid issue they need to have a fastq extension

lpantano commented 8 years ago

thanks for looking into that! i will add a proper handler there!

On 02/03/2016 11:14 AM, filicado wrote:

Closed #13 https://github.com/lpantano/seqcluster/issues/13.

— Reply to this email directly or view it on GitHub https://github.com/lpantano/seqcluster/issues/13#event-537777463.