User Activity

  • Posted a comment on ticket #68 on mocat

    The MOCAT2 GitHub version is an unsupported developmental version. You need to add the MOCAT/unpublished folder to you PERL5LIB UNIX variable. Have a look at your ~/.bashrc and add the folder to it there. In general MOCAT2 isn't always user friendly and requires quite some UNIX experience. Good luck! On Wed, Aug 2, 2017 at 01:02 suraj metha surajmetha@users.sf.net wrote: [tickets:#68] Error while using MOCAT2 pipeline Status: New Created: Wed Aug 02, 2017 05:02 AM UTC by suraj metha Last Updated:...

  • Posted a comment on ticket #42 on mocat

    Just copy the folders into the same folders as you installed MOCAT. No need to re-run any other scripts. Please note that I cannot provide any support beyond this right now as I'm not actively developing MOCAT anymore. Good luck! Jens Roat Kultima, Ph.D. Computational Scientist Janssen Human Microbiome Institute Janssen Pharmaceuticals 255 Main Street, 10th Floor Cambridge, MA 02142 On Mon, Jul 31, 2017 at 10:13 AM, Silas Kieser silask@users.sf.net wrote: Can you explain me again, what should I do...

  • Posted a comment on ticket #67 on mocat

    If you download the version from the github under MOCAT2 it support SLURM. On Mon, Jul 31, 2017 at 07:57 Silas Kieser silask@users.sf.net wrote: [tickets:#67] Mocat excedes memory limit on a SLURM cluster Status: New Labels: memory Created: Mon Jul 31, 2017 11:57 AM UTC by Silas Kieser Last Updated: Mon Jul 31, 2017 11:57 AM UTC Owner: nobody Hallo, I've installed Mocat on our university cluster. Unfortunately they have only Slurm as queing system. I'm doing a test run of Mocat with two samples....

  • Posted a comment on ticket #66 on mocat

    ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround a code snippet with "~~~~"?Edit your ~/.bashrc file to make sure PERL5LIB includes the path to the MOCAT src folder. Consider copying the MOCAT files to either of those folders mentioned. Make sure you don't have two perl installations. This is a system specific error that we wouldn't be able to solve. If neither of the above works I suggest contacting your system admin. On Fri, Jul 28, 2017 at 07:48 sanjana <sanjs85@users.sf.net>...

  • Posted a comment on ticket #64 on mocat

    Thank you! On Thu, Jul 27, 2017 at 05:00 Marta Pozuelo mpozud00@users.sf.net wrote: [tickets:#64] Read trimming error with three files Status: New Created: Thu Jul 27, 2017 09:00 AM UTC by Marta Pozuelo Last Updated: Thu Jul 27, 2017 09:00 AM UTC Owner: nobody Hi! When I was running my samples with MOCAT, I have found that if you use three files pair1, pair2 and single, there was an error because it didn't detected two of the files. Having a look at the script is because of the variable $ending that...

  • Posted a comment on ticket #65 on mocat

    There are a couple of known bugs in some of the scripts. I advise to look through the various bug reports on this site. I also suggest you to in each command individually and look at the output log files under logs/---/samples. Unfortunately I don't currently have the bandwidth to look into these issues further. On Thu, Jul 27, 2017 at 11:56 Alexandre B. de Menezes ademenez@users.sf.net wrote: [tickets:#65] Pipeline installation error Status: New Created: Thu Jul 27, 2017 03:56 PM UTC by Alexandre...

  • Posted a comment on ticket #63 on mocat

    Again, there's unfortunately no way of us knowing what went wrong solely based on a list of files. zip your entire logs folder and provide it. On Mon, Jul 10, 2017 at 08:05 linyunzheng linyunzheng@users.sf.net wrote: I rerun the pipeline,but it still doesn't goes well.The output file is GENE_CATALOGS,if it went well,there shuold be a test_name folder ,test_name.faa and test_name.fna in this output,and in the test_name folder there have [padded_catalog][catalog][temp],but when I performed this make_gene_catalog...

  • Posted a comment on ticket #63 on mocat

    The information your provided isn't enough to find the cause of the error. Unless you can resolve the error by looking through the error logs in the logs folder by yourself, I suggest you remove the data folder and it's content and re-run everything from scratch. On Thu, Jul 6, 2017 at 10:30 linyunzheng linyunzheng@users.sf.net wrote: [tickets:#63] error in make_gene_catalog Status: New Labels: make gene catalog Created: Thu Jul 06, 2017 02:30 PM UTC by linyunzheng Last Updated: Thu Jul 06, 2017...

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