Error with TEST_DATA

[dwightkuo]

I'm trying to use Shortstack 3.7.1 with the data provided in TEST_DATA.tgz. I get the following error after Adapter trimming: ./ShortStack --adapter CTGTAGGC --readfile SRR051927.fastq --outdir test1 --genomefile Athaliana_167.fa

Tue Feb 7 13:53:31 PST 2017 Adapter trimming input reads file TEST_DATA/SRR051927.fastq with adapter CTGTAGGC Complete: 4949843 out of 5703995 reads successfully trimmed FATAL in sub-routine get_read_s_aln : Could not determine format of reads file test1/SRR051927.fastq_trimmed

[MikeAxtell]

dang it. Sorry about that. I'll get it fixed ASAP.

On Tue, Feb 7, 2017 at 5:06 PM, dwightkuo notifications@github.com wrote:

I'm trying to use Shortstack 3.7.1 with the data provided in TEST_DATA.tgz. I get the following error after Adapter trimming: ./ShortStack --adapter CTGTAGGC --readfile SRR051927.fastq --outdir test1 --genomefile Athaliana_167.fa

Tue Feb 7 13:53:31 PST 2017 Adapter trimming input reads file TEST_DATA/SRR051927.fastq with adapter CTGTAGGC Complete: 4949843 out of 5703995 reads successfully trimmed FATAL in sub-routine get_read_s_aln : Could not determine format of reads file test1/SRR051927.fastq_trimmed

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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell

[MikeAxtell]

Fixed with release 3.7.2

[MikeAxtell]

Hi Dwight. Did you post this to the wrong github thread? I don't recognize this as ShortStack related errors. These look like jbrowse or galaxy issues?

Best, Mike Axtell

On Wed, Feb 8, 2017 at 11:48 AM, dwightkuo notifications@github.com wrote:

Here's the full error message:

Fatal error: Exit code 1 ()

INFO:jbrowse:Processing Default / GFF3 file from data 48 Attempt to reload Scalar/Util.pm aborted. Compilation failed in require at /remote/RMS/users/galaxyd/job_ workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/File/Temp.pm line 18. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/File/Temp.pm line 18. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/ExternalSorter.pm line 42. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/ExternalSorter.pm line 42. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm line 8. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm line 8. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/base.pm line 99. ...propagated at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/base.pm line 108. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 18. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/flatfile-to-json.pl line 7. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job working_directory/013/13750/conda-env/opt/jbrowse/bin/flatfile-to-json.pl line 7. Traceback (most recent call last): File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 709, in for key in keys: File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 578, in process_annotations track['conf']['options']['gff']) File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 538, in add_features self.subprocess_check_call(cmd) File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 335, in subprocess_check_call subprocess.check_call(command, cwd=self.outdir) File "/remote/RMS/users/galaxyd/job_working_directory/013/ 13750/conda-env/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['perl', '/remote/RMS/users/galaxyd/job_working_directory/013/ 13750/conda-env/opt/jbrowse/bin/flatfile-to-json.pl', '--gff', '/remote/RMS/users/galaxyd/files/094/dataset_94717.dat', '--trackLabel', ' 955cdeb547221b777c786d630d2d8f51_0', '--key', 'GFF3 file from data 48', '--clientConfig', '{"className": "feature", "color": "#a6cee3", "description": "note,description", "label": "name,id"}', '--trackType', 'JBrowse/View/Track/CanvasFeatures', '--config', '{"category": "Default", "menuTemplate": [{}, {}, {}, {}], "key": "GFF3 file from data 48", "label": "955cdeb547221b777c786d630d2d8f51_0"}']' returned non-zero exit status 255

On Tue, Feb 7, 2017 at 6:47 PM, Mike Axtell notifications@github.com wrote:

Fixed with release 3.7.2

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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell

[MikeAxtell]

It popped through to my email github relays those emails quickly, no worries!

On Wed, Feb 8, 2017 at 11:55 AM, dwightkuo notifications@github.com wrote:

Yes that's right, I posted it to the wrong widow but thought I deleted the comment?

On Feb 8, 2017 08:51, "Mike Axtell" notifications@github.com wrote:

Hi Dwight. Did you post this to the wrong github thread? I don't recognize this as ShortStack related errors. These look like jbrowse or galaxy issues?

Best, Mike Axtell

On Wed, Feb 8, 2017 at 11:48 AM, dwightkuo notifications@github.com wrote:

Here's the full error message:

Fatal error: Exit code 1 ()

INFO:jbrowse:Processing Default / GFF3 file from data 48 Attempt to reload Scalar/Util.pm aborted. Compilation failed in require at /remote/RMS/users/galaxyd/job_ workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/File/Temp.pm line 18. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/File/Temp.pm line 18. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/ExternalSorter.pm line 42. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/ExternalSorter.pm line 42. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm line 8. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm line 8. Compilation failed in require at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/base.pm line 99. ...propagated at /remote/RMS/users/galaxyd/job workingdirectory/013/13750/conda-env/lib/perl5/5.22.0/base.pm line 108. BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job working_directory/013/13750/conda-env/opt/jbrowse/bin/../ src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 18.

Compilation failed in require at /remote/RMS/users/galaxyd/job_ working_directory/013/13750/conda-env/opt/jbrowse/bin/flat file-to-json.pl

line 7.

BEGIN failed--compilation aborted at /remote/RMS/users/galaxyd/job_ working_directory/013/13750/conda-env/opt/jbrowse/bin/flat file-to-json.pl line 7. Traceback (most recent call last): File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 709, in for key in keys: File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 578, in process_annotations track['conf']['options']['gff']) File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 538, in add_features self.subprocess_check_call(cmd) File "/opt/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/ db5fe5a3176a/jbrowse/jbrowse.py", line 335, in subprocess_check_call subprocess.check_call(command, cwd=self.outdir) File "/remote/RMS/users/galaxyd/job_working_directory/013/ 13750/conda-env/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['perl', '/remote/RMS/users/galaxyd/job_working_directory/013/ 13750/conda-env/opt/jbrowse/bin/flatfile-to-json.pl', '--gff', '/remote/RMS/users/galaxyd/files/094/dataset_94717.dat', '--trackLabel', ' 955cdeb547221b777c786d630d2d8f51_0', '--key', 'GFF3 file from data 48', '--clientConfig', '{"className": "feature", "color": "#a6cee3", "description": "note,description", "label": "name,id"}', '--trackType', 'JBrowse/View/Track/CanvasFeatures', '--config', '{"category": "Default", "menuTemplate": [{}, {}, {}, {}], "key": "GFF3 file from data 48", "label": "955cdeb547221b777c786d630d2d8f51_0"}']' returned non-zero exit status 255

On Tue, Feb 7, 2017 at 6:47 PM, Mike Axtell notifications@github.com wrote:

Fixed with release 3.7.2

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.

-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell

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