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churchlab / millstone

Genome engineering and analysis software
http://churchlab.github.io/millstone/
MIT License
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bwa mem really doesn't like '(' in ref genome #308

Open mnapolitano89 opened 10 years ago

mnapolitano89 commented 10 years ago

I think. clears up if ( removed from path. testing further once I reinstance with more ram (millstone really doesn't like it when it runs out of memory and gets very quickly into an unusable state -in particular if bwamem doesn't run after sample upload it gets "stuck") /bin/bash: -c: line 0: syntax error near unexpected token (' /bin/bash: -c: line 0:tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -' ==START OF ALIGNMENT PIPELINE FOR EcM2.1, (378f1302) ==tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -Traceback (most recent call last): File "/home/ubuntu/millstone/genome_designer/pipeline/read_alignment.py", line 138, in align_with_bwa_mem shell=True, executable=BASH_PATH) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -' returned non-zero exit status 1 ==END OF ALIGNMENT PIPELINE==

glebkuznetsov commented 10 years ago

Yeah we should rename imported files using this method: https://github.com/churchlab/millstone/blob/master/genome_designer/utils/__init__.py#L97

On Thu, Apr 24, 2014 at 6:23 PM, mnapolitano89 notifications@github.comwrote:

I think. clears up if ( removed from path. testing further once I reinstance with more ram (millstone really doesn't like it when it runs out of memory and gets very quickly into an unusable state -in particular if bwamem doesn't run after sample upload it gets "stuck") /bin/bash: -c: line 0: syntax error near unexpected token (' /bin/bash: -c: line 0:tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -' ==START OF ALIGNMENT PIPELINE FOR EcM2.1, (378f1302) ==tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -Traceback (most recent call last): File "/home/ubuntu/millstone/genome_designer/pipeline/read_alignment.py", line 138, in align_with_bwa_mem shell=True, executable=BASH_PATH) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'tools/bwa/bwa mem -t 1 -M /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/ref_genomes/08f336a2/tmpgH7euk_sequence (2).fa /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmpqzsoUo_EcM2.1_R2 /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/3c8a3928/samples/75eb55ce/tmp0rOu25_EcM2.1_R1 | tools/samtools/samtools view -bS -' returned non-zero exit status 1 ==END OF ALIGNMENT PIPELINE==

— Reply to this email directly or view it on GitHubhttps://github.com/churchlab/millstone/issues/308 .

mnapolitano89 commented 10 years ago

or spaces. next on my list of things to do?

mnapolitano89 commented 10 years ago

as a work around file uploads should avoid whitespace or other non-alphanumeric file names

glebkuznetsov commented 10 years ago

Yeah that function basically replaces anything that's not an alphanumeric char with an underscore. It uses the regular expression shorthand \W which is equivalent to anything not in [a-zA-Z0-9_].

On Thu, Apr 24, 2014 at 6:52 PM, mnapolitano89 notifications@github.com wrote:

as a work around file uploads should avoid whitespace or other non-alphanumeric file names

— Reply to this email directly or view it on GitHub.

glebkuznetsov commented 10 years ago

Yeah this is a really important bug to fix if you want to take it on.

On Thu, Apr 24, 2014 at 6:54 PM, Gleb Kuznetsov gleb.kuznetsov@gmail.com wrote:

Yeah that function basically replaces anything that's not an alphanumeric char with an underscore. It uses the regular expression shorthand \W which is equivalent to anything not in [a-zA-Z0-9_].

On Thu, Apr 24, 2014 at 6:52 PM, mnapolitano89 notifications@github.com wrote:

as a work around file uploads should avoid whitespace or other non-alphanumeric file names

— Reply to this email directly or view it on GitHub.