Closed filicado closed 8 years ago
sorry stupid issue they need to have a fastq extension
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.
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