mocat Activity
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Activity for mocat
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Nailah Latif Ahmed posted a comment on ticket #97
But at the end of the "tutorial" page, I click in "2 - Generate taxonomic profiles (mOTU-LOG, specI & NCBI)" for the full tutorial, and the link happens to be "page not found", the same https://mocat.embl.de/~kultima/mOTU/tutorial.html
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MOCAT posted a comment on ticket #97
See the notice that MOCAT is not longer maintained at: https://mocat.embl.de/index.html And a tutorial is at: https://mocat.embl.de/tutorial.html On Fri, Mar 4, 2022 at 5:08 PM Nailah Latif Ahmed nailahla@users.sourceforge.net wrote: [tickets:#97] Taxonomic profile tutorial Status: New Created: Fri Mar 04, 2022 04:08 PM UTC by Nailah Latif Ahmed Last Updated: Fri Mar 04, 2022 04:08 PM UTC Owner: MOCAT I am having a hard time finding the tutorial for taxonomic profiling. I already have my metagenomic...
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Taxonomic profile tutorial
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Unfortunately I no longer have the resources to support these bug reports. I hope you’re able to solve it. On Sun, 18 Oct 2020 at 09:06, Francesca De Filippis fdefilippis@users.sourceforge.net wrote: [tickets:#96] MOCAT2 does not find scripts folder Status: New Created: Sun Oct 18, 2020 07:06 AM UTC by Francesca De Filippis Last Updated: Sun Oct 18, 2020 07:06 AM UTC Owner: nobody Attachments: MOCAT.cfg (5.8 kB; application/octet-stream) Hi there I’m trying to use MOCAT2 on my soil metagenomes. I’d...
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Francesca De Filippis created ticket #96
MOCAT2 does not find scripts folder
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ERXIATI PAERHATI created ticket #95
Lacking last version MOCAT2 cfg file documentation
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Unfortunately I can no longer support individual bug reports of this kind. I encourage you to look in the log folders and try to make it out. Probably a step before fails. I understand it’s a bit of a jungle and I’m sorry I don’t have the bandwidth to support you further. On Wed, 1 Jul 2020 at 12:06, ERXIATI PAERHATI erxatferhat@users.sourceforge.net wrote: [tickets:#94] runMOCAT.sh stops halfway Status: New Created: Wed Jul 01, 2020 10:06 AM UTC by ERXIATI PAERHATI Last Updated: Wed Jul 01, 2020...
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runMOCAT.sh stops halfway
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Regina Umarova posted a comment on ticket #93
Hello, Thank you for your reply. I have found the answer on MOCAT GitHub page. It can be found below on case someone is interested. You need to add the following line in MOCAT.cfg file 'GLOBAL SETTINGS' MOCAT_data_dir: /usr/desired_filder Hope it will be helpful Best, Regina
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Hi, I no longer support MOCAT unfortunately and there’s no other developer. I can’t remember. I doubt it. Possibly make a soft link to another writable folder for the user and then have admin copy those new files to update the original data folder. There’s a setting for making a specific data_rownames folder you may also want to look into. Can’t help further this at this point. Good luck!! On Thu, 5 Dec 2019 at 17:56, Regina Umarova rumarova@users.sourceforge.net wrote: [tickets:#93] make_gene_catalog...
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make_gene_catalog - sample.padded files
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I no longer actively support MOCAT. I advise to run it on UNIX. Regards, Jens On Tue, 3 Sep 2019 at 16:38, Jan Macher tamandua@users.sourceforge.net wrote: [tickets:#92] fastq_trim_filter_v5_EMBL_OSX Status: New Created: Tue Sep 03, 2019 02:38 PM UTC by Jan Macher Last Updated: Tue Sep 03, 2019 02:38 PM UTC Owner: MOCAT Hello I tried using MOCAT2 on OSX, but the readtrimfilter step fails because MOCAT is looking for the "fastq_trim_filter_v5_EMBL_OSX" image, which does not exist in MOCAT/bin. I know...
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JM created ticket #92
fastq_trim_filter_v5_EMBL_OSX
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Neetha posted a comment on ticket #91
The issue has been resolved. It was due to perl DBI module missing which was required by filterBlastReport.pl script though it is strange that this error did not show up in the logs. fixed it by installing the module.
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annotate_gene_catalog no results
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huangjiandong modified a comment on ticket #79
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Output function abundance table？
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Many thanks for your help. These files look like summary files. Right? Can these steps generate a detailed classification abundance table? Just like ARDB database(MOCAT/functional_annotations/ARDB.txt)： AAC2I Resistance type: netilmicin AAC2I Resistance type: tobramycin AAC2I Resistance type: 6_n_netilmicin AAC2I Resistance type: dibekacin AAC2I Resistance type: gentamicin AAC2IA Resistance type: netilmicin AAC2IA Resistance type: tobramycin AAC2IA Resistance type: 6_n_netilmicin
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These step don’t generate files in the output folder (only taxonomic profiling does). See previous comments to use the mm.dist.among.unique files. On Sat, 6 Apr 2019 at 18:56, huangjiandong hjd@users.sourceforge.net wrote: I met the same problem. Have you solved it? There are no files in the "OUTPUT" folder. Thanks. [tickets:#79] The output of function profiles Status: New Labels: profiles Created: Sat Jan 13, 2018 08:42 AM UTC by jxcui Last Updated: Sat Feb 16, 2019 09:42 AM UTC Owner: nobody Attachments:...
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I met the same problem. Have you solved it? There are no files in the "OUTPUT" folder. Thanks.
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Look for that line in MOCAT.pl and add a ‘#’ to the beginning of it to comment it. There may be a few things you have to add manually to the MOCAT.cfg as well. Good luck! On Fri, 15 Mar 2019 at 15:46, Marcela Agu maf2371@users.sourceforge.net wrote: Hello, I know MOCAT is no longer being supported but I was wondering if you were able to solve the MOCATUnpublished::Launch() problem? I am trying to use MOCAT and I get the same thing Marcela [tickets:#86] MOCAT.cfg not working Status: New Labels: mocat.cfg...
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Dattatray Mongad created ticket #88
Out of memory error during assembly
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Marcela Agu posted a comment on ticket #86
Hello, I know MOCAT is no longer being supported but I was wondering if you were able to solve the MOCATUnpublished::Launch() problem? I am trying to use MOCAT and I get the same thing Marcela
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Hi, I've solved the issue on an Amazon Cloud instance by doing this: 1. Install CPAN: sudo yum install perl-CPAN 2. Install gcc: sudo yum install gcc 3. Install three modules: cpan -i YAML cpan -i -f File::Sync cpan -i File::Slurp
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jxcui posted a comment on ticket #79
Thanks. You can see that values add up to were less than "mapped", is there any problems? Futhermore, how to normalize?
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Santanu Das created ticket #87
Error in starting project
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Nathaniel Chu posted a comment on ticket #80
I ran into the same problem as Peter and Adam. I followed Peter's instructions commenting out line 51 in Functional.pm $line[$i] = ''; and then adding the lines given in Peter's earlier post. I found that one addition was necessary to his code, which was to replace @cogs = '' x $line_parts; with @cogs = '' x my $line_parts; as this was the first reference to $line_parts. I also tried with some older Perl version, but ran into more problems than solutions there.
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Peter Bazeley posted a comment on ticket #80
Hi Adam, As the author pointed it was a Perl issue. I installed MOCAT with another account and had no issues. So I would talk to your admin about having the correct version of Perl in your PATH, and use that edit as a last resort. Also the lack of indentation is just my laziness... -Peter
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This issue is likely due to changes in newer versions of perl. See the previous solution posted. On Wed, 27 Jun 2018 at 11:02, Adam Blanchard addyblanch@users.sourceforge.net wrote: Hi Peter, I am having the same issue. Just wondered if it would be a copy and paste job for that new line. Wasn't sure about indentation in perl. Adam [tickets:#80] Functional.pm line 51: "Modification of read-only value attempted" Status: New Labels: profiling Created: Wed Jan 17, 2018 04:52 AM UTC by Peter Bazeley Last...
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Adam Blanchard posted a comment on ticket #80
Hi Peter, I am having the same issue. Just wondered if it would be a copy and paste job for that new line. Wasn't sure about indentation in perl. Adam
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Marta Pozuelo posted a comment on ticket #79
Many thanks for your help. Marta
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Because those files have read mapping to multiple locations distributed according to the abundances of reads mapping uniquely, and those files have thus more accurate abundance estimates of genes, species and functions. On Thu, 14 Jun 2018 at 14:55, Marta Pozuelo mpozud00@users.sourceforge.net wrote: Why is it recommended to use those files instead the ones without mm.dist.unique? Thanks for your response Marta [tickets:#79] The output of function profiles Status: New Labels: profiles Created: Sat...
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Why is it recommended to use those files instead the ones without mm.dist.unique? Thanks for your response Marta
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Anuradha Ravi modified a comment on ticket #86
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Hello I understand it is beyond your scope to assist on a project that is finished but your tool seems to help me with the task at hand. your solution was valid and it worked. However, I get an internal error which is beyond my understanding-- My command was MOCAT.pl -sf my.samples -rtf I get this error: Undefined subroutine &MOCATUnpublished::Launch called at /mnt/volume_3/mocat2/stable/2.1.3/src/MOCAT.pl line 688. I will be grateful if you could help me with this. Thanks! Anu
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Add it t the confit file or remove it from the MOCAT.pl file (search for it). I can't help more than this now. On Wed, 6 Jun 2018 at 15:49, Anuradha Ravi anuravi@users.sourceforge.net wrote: Hello, thank you for your quick reply. My MOCAT files are in the 2.1.3 and I took the config file which is in the "Getting started" folder in that directory. Does this mean, my Mocat that was installed is of an older version? I dont think my MOCAT is of an older version since it shows that the version (2.1.3)...
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Hello, thank you for your quick reply. My MOCAT files are in the 2.1.3 and I took the config file which is in the "Getting started" folder in that directory. Does this mean, my Mocat that was installed is of an older version? I dont think my MOCAT is of an older version since it shows that the version (2.1.3) when I start on the tool. I used git clone to install MOCAT in my server. I look forward for your comment Anu
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You haven't updated to use the confit file that ships with version 2.1.3. You're using an old confit file for version 2.0 likely. Change to the new version. On Wed, 6 Jun 2018 at 15:12, Anuradha Ravi anuravi@users.sourceforge.net wrote: [tickets:#86] MOCAT.cfg not working Status: New Labels: mocat.cfg file mocat.pl Created: Wed Jun 06, 2018 01:12 PM UTC by Anuradha Ravi Last Updated: Wed Jun 06, 2018 01:12 PM UTC Owner: MOCAT Attachments: MOCAT.cfg (9.0 kB; application/octet-stream) Hello I am having...
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MOCAT.cfg not working
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Values add up to more than "mapped" because a gene can belong to multiple KOs. There's no specific manual. It's recommended to use the mm.dist.among.unique files. On Mon, 4 Jun 2018 at 17:41, Marta Pozuelo mpozud00@users.sourceforge.net wrote: I am also interested in this fact. Is it possible for someone to answer? Thank you. Marta [tickets:#79] The output of function profiles Status: New Labels: profiles Created: Sat Jan 13, 2018 08:42 AM UTC by jxcui Last Updated: Sat Jan 13, 2018 08:42 AM UTC...
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I am also interested in this fact. Is it possible for someone to answer? Thank you. Marta
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Assembly revision had been deprecated and I advise not to use it. On Fri, 25 May 2018 at 10:38, Hugo_Ji hugoji@users.sourceforge.net wrote: [tickets:#85] Error when merge bam file Status: New Labels: Assembly revision Created: Fri May 25, 2018 08:38 AM UTC by Hugo_Ji Last Updated: Fri May 25, 2018 08:38 AM UTC Owner: MOCAT Attachments: - MOCATJob_assembly_revision.SRR6000905.SRR6000905_list_2018May23_221925.log (98.3 kB; text/x-log) Hello,I was using MOCAT2 to assembly my metagenomics sequence file.And...
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Hugo_Ji created ticket #85
Error when merge bam file
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The IGC catalog has been annotated to eggNOG and about 20 other databases, which makes it possible to summarize gene abundances at all those levels. And this is done automatically by MOCAT in the functional step. Don't know what you mean by FMG. On Fri, Apr 6, 2018 at 00:10 Peter Bazeley theoark@users.sourceforge.net wrote: Hi. So in my quest to find abundances for the FMGs in each sample, it appears that there's no good way to associate COGs with the IGC catalog (or is there?). So the alternative...
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Hi. So in my quest to find abundances for the FMGs in each sample, it appears that there's no good way to associate COGs with the IGC catalog (or is there?). So the alternative appears to be to take the gene.prediction.assembly result sequences, extract the ones that were matched with the FMGs, and align those to the IGC catalog. Does that sound reasonable? Thanks, Peter
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Not for taxanomic comparison but as a way to deal with compositional bias. Wouldn't this give a kind of average gene abundane per species, or am I way off?
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I would advise to use the mOTUs and the built in taxonomic pipeline for taxonomic abundances. I don't see the logic of mixing single gene abundances and taxonomic abundances. On Mon, Apr 2, 2018 at 17:30 Peter Bazeley theoark@users.sourceforge.net wrote: [tickets:#84] Abundance scaled by FMG abundances? Status: New Labels: FMG Created: Mon Apr 02, 2018 03:30 PM UTC by Peter Bazeley Last Updated: Mon Apr 02, 2018 03:30 PM UTC Owner: MOCAT Hello, Any advice for using the abundances for the 40 marker...
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Abundance scaled by FMG abundances?
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I don't know where Filr::Sync is installed when you installed it. But look inside all of the folders in the @INC. My guess is that somehow CPAN installed it into a different folder. There are some instructions on the download page of the official MOCAT website that you can try to (re)install sync module. On Sat, Feb 24, 2018 at 03:10 Patrick Seed pseed@users.sourceforge.net wrote: [tickets:#83] File::Sync module issue Status: New Created: Sat Feb 24, 2018 02:10 AM UTC by Patrick Seed Last Updated:...
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Patrick Seed created ticket #83
File::Sync module issue
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It's the porportion of the gene/contig/sequence that has at least 1x coverage, ie a read covering that piece. Very basic in that sense. Jens Roat Kultima, Ph.D. Computational Scientist Janssen Human Microbiome Institute Janssen Pharmaceuticals 255 Main Street, 10th Floor Cambridge, MA 02142 On Wed, Feb 21, 2018 at 11:38 AM, Peter Bazeley theoark@users.sourceforge.net wrote: Do you have more details of how this is calculated? Is it just a proportion of the gene length that has any read alignment or...
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Do you have more details of how this is calculated? Is it just a proportion of the gene length that has any read alignment or is it weighted by the number of reads? I'm wondering how to interpret these. Thanks. On Mon, Feb 12, 2018 at 4:21 AM, MOCAT <mocat-pipeline@users.sourceforge.net wrote: No. These are the horizontal gene coverages (what fraction of the gene has coverage), which is not related of horizontal gene transfers. On Mon, Feb 12, 2018 at 05:25 Peter Bazeley theoark@users.sourceforge.net...
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Genome size normalization?
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No. These are the horizontal gene coverages (what fraction of the gene has coverage), which is not related of horizontal gene transfers. On Mon, Feb 12, 2018 at 05:25 Peter Bazeley theoark@users.sourceforge.net wrote: [tickets:#81] horizontal gene coverage Status: New Labels: horizontal Created: Mon Feb 12, 2018 04:25 AM UTC by Peter Bazeley Last Updated: Mon Feb 12, 2018 04:25 AM UTC Owner: MOCAT Hello, Do the horiztonal gene abundance files refer to horiztonal gene transfers? If so, are these from...
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horizontal gene coverage
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Hi, I ended up just commenting out line 51, and changing line 56 to: " my @line_parts = scalar @line; my @cogs; if (defined($line[$i])) { @cogs = split /[,|]/, $line[$i]; } else { @cogs = '' x $line_parts; } " and this runs fine. HTH, Peter
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Functional.pm line 51: "Modification of read-only value attempted"
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The output of function profiles
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the
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Unfortunately I don't have the bandwidth for detailed support. I suggest you read the manual, where it's described how to use databases split into multiple parts. In this case you have to do "-s IGC.1 IGC.2" and same command with "-p" for profiling. Good luck with your analyses and unfortunately, again, I suggest reading the manual! On Mon, Jan 8, 2018 at 15:39 Peter Bazeley theoark@users.sf.net wrote: I downloaded the IGC.zip file from the MOCAT website, unzipped it, and when I try: MOCAT.pl -sf...
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I downloaded the IGC.zip file from the MOCAT website, unzipped it, and when I try: MOCAT.pl -sf my.samples -s IGC -screened_files I get: Mon Jan 8 09:35:30 2018: PERFORMING SCREEN USING DATABASE... Mon Jan 8 09:35:30 2018: Checking files... OK! Mon Jan 8 09:35:30 2018: Creating screen jobs... ERROR & EXIT: IGC is not a valid database path at <mocat dir="">/src/MOCATScreen.pm line 134. It works if I copy the map files to IGC.1.functional.map and use: MOCAT.pl -sf my.samples -s IGC.1 -screened_files...
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Just run the profiling step with the same command line as the screening step. E.g., replace "-screen" with "-profile". MOCAT knows what to do. No need to change any files. On Mon, Jan 8, 2018 at 05:12 Peter Bazeley theoark@users.sf.net wrote: [tickets:#77] IGC.1 and IGC.2 Status: New Labels: IGC Created: Mon Jan 08, 2018 04:11 AM UTC by Peter Bazeley Last Updated: Mon Jan 08, 2018 04:11 AM UTC Owner: MOCAT Hello, I am trying to profile my reads against IGC and notice there is only a single .functional.map...
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IGC.1 and IGC.2
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Thanks, this solved the issue. Appreciate your help.
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Hello, To piggy-back off of this ticket, if I want to do the above but also filter against hg19 prior to IGC, would I use the following commands: MOCAT.pl -sf my.samples -rtf MOCAT.pl -sf my.samples -s hg19 MOCAT.pl -sf my.samples -s IGC -r hg19 MOCAT.pl -sf my.samples -f IGC MOCAT.pl -sf my.samples -p IGC -mode functional Thank you for your assistance, Peter
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I'd to the latter with /1 and /2. On Fri, Jan 5, 2018 at 22:56 Peter Bazeley theoark@users.sf.net wrote: Or should I convert to this format: @HWUSI-EAS100R:6:73:941:1973#0/1 [tickets:#76] RTF Saving PE reads as single FQ Status: New Labels: RTF Created: Fri Jan 05, 2018 05:01 PM UTC by Peter Bazeley Last Updated: Fri Jan 05, 2018 09:50 PM UTC Owner: MOCAT Hello, I have PE data (files named "lane1.1.fq" and "lane1.2.fq") and have set "MOCAT_paired_end" to "yes" in the config file and after running...
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Or should I convert to this format: @HWUSI-EAS100R:6:73:941:1973#0/1
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My headers (1 from each PE file) looks like this: @K00136:435:HGL7GBBXX:4:1104:16985:30433 1:N:0 @K00136:435:HGL7GBBXX:4:1104:16985:30433 2:N:0 This looks similar to the wikipedia page for Casava 1.8: " With Casava 1.8 the format of the '@' line has changed: @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG " except no index sequence at the end. Should I add a dummy sequence at the end? Thanks for your help, Peter
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It's possible the headers in your fast files aren't of standard header format. Look at the Wikipedia page for the fast format and ensure the reads are named correctly to one of the formats. On Fri, Jan 5, 2018 at 18:01 Peter Bazeley theoark@users.sf.net wrote: [tickets:#76] RTF Saving PE reads as single FQ Status: New Labels: RTF Created: Fri Jan 05, 2018 05:01 PM UTC by Peter Bazeley Last Updated: Fri Jan 05, 2018 05:01 PM UTC Owner: MOCAT Hello, I have PE data (files named "lane1.1.fq" and "lane1.2.fq")...
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RTF Saving PE reads as single FQ
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Jose posted a comment on ticket #70
Hi Jxcui! Thank you very much for the feedback! Yes... it seems not a very tested pipeline anyway...
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hi Jose, I found the problem. The parameter "-screened_files" for screen was missing in the file "MOCAT/scripts/assemble_revise_predict_genes_with_hg19_screen". You shoud add "-screened_files" to the line "[command] -s hg19 -identity 90". Hope this helps. Though there are still other problems in subsequent steps that I can't solve.
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As Jose said, we used the wrapper script runMOCAT.sh with the parameter "4：assemble_revise_predict_genes_with_hg19_screen" , and in the log file, -r hg19 was specified.
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No, I didn't solve it, sorry!
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No, I didn't. Sorry!
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As you can clearly see in the logs that I uploaded, -r hg19 was specified, but MOCAT crashed miserabily: EXECUTE COMMAND : -sf /scratch/MOCAT/MOCAT.samples -cfg /scratch/MOCAT/logs/tmp//user.MOCAT.samples.20170808_224339.assemble_revise_predict_genes_with_hg19_screen/MOCAT.cfg -a -r hg19
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You have to specify -r hg19 or -r reads.processed On Wed, Dec 13, 2017 at 04:29 jxcui cjx13@users.sf.net wrote: hey, I met the same problem as yours. have you solved it? [tickets:#70] hg19 DB not recognised in the assembly stage Status: New Labels: assembly runMOCAT Created: Tue Aug 08, 2017 09:49 PM UTC by Jose Last Updated: Tue Aug 08, 2017 09:49 PM UTC Owner: MOCAT Attachments: logs.tar.gz (11.1 kB; application/x-gzip) Hello MOCAT team, First of all, thanks for puting together this amazing pipeline....
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hey, I met the same problem as yours. have you solved it?
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Claire Hoede created ticket #75
a chomp $ending is missing in MOCATReadTrimFilter_aux.pl
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bug when there is 3 .fq file per sample
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Again, Please read the documentation. I can't remember he command by heart. It's -soap. On Fri, Nov 10, 2017 at 20:08 Joshua Gray jgray@users.sf.net wrote: Unfortunately, this gave the same error. MOCAT MODULE MODE ACTIVATED MODULE = screen ERROR & EXIT: Tried to launch module 'screen', but could not find expected file /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/screen/screen.sh at /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072. Using your suggestion, I edited...
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Joshua Gray posted a comment on ticket #73
Unfortunately, this gave the same error. MOCAT MODULE MODE ACTIVATED MODULE = screen ERROR & EXIT: Tried to launch module 'screen', but could not find expected file /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/screen/screen.sh at /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072. Using your suggestion, I edited the appropriate line of the runMOCAT.sh file to read: -sf my.samples -screen hg19 -screened_files Josh
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Please read the MOCAT documentation. The -s option is deprecated for the github version. Use -screen. On Fri, Nov 10, 2017 at 10:55 Joshua Gray jgray@users.sf.net wrote: Also, here are the tryMOCAT.sh file and the MOCAT.cfg file. Attachments: MOCAT.cfg (9.4 kB; application/octet-stream) tryMOCAT.sh (197 Bytes; application/octet-stream) [tickets:#73] Issue with latest development version on SLURM cluster Status: New Labels: SLURM development assembly Created: Fri Nov 10, 2017 03:53 PM UTC by Joshua...
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Also, here are the tryMOCAT.sh file and the MOCAT.cfg file.
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Issue with latest development version on SLURM cluster
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As the message says, you have to specify which READS you've used. In this case -r reads.processed Jens Roat Kultima, Ph.D. Computational Scientist Janssen Human Microbiome Institute Janssen Pharmaceuticals 255 Main Street, 10th Floor Cambridge, MA 02142 On Wed, Sep 20, 2017 at 9:50 AM, Zewei Song zewei@users.sf.net wrote: [tickets:#72] Error on the second commnad (-a) in the manual Status: New Created: Wed Sep 20, 2017 01:50 PM UTC by Zewei Song Last Updated: Wed Sep 20, 2017 01:50 PM UTC Owner:...
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Zewei Song created ticket #72
Error on the second commnad (-a) in the manual
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Outfiles of taxonomic profiling linked to the wrong files
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Thanks, updated on the github version: https://github.com/mocat2/mocat2
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Jian-Huan Chen created ticket #71
Outfiles of taxonomic profiling linked to the wrong files
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hg19 DB not recognised in the assembly stage
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sanjana created ticket #69
Annotate_gene_catalog
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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:...
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suraj metha created ticket #68
Error while using MOCAT2 pipeline
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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...
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Silas Kieser posted a comment on ticket #42
Can you explain me again, what should I do to use the developpment version? Should I use dev/public or dev/unpublished Which setup scripts do I have to use? Kidn regards Silas
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Super. I'll try this. You can close the ticket. From: MOCAT [mailto:mocat-pipeline@users.sf.net] Sent: Montag, 31. Juli 2017 15:30 To: [mocat:tickets] 67@tickets.mocat.p.re.sf.net Subject: [mocat:tickets] Re: #67 Mocat excedes memory limit on a SLURM cluster 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 silask@users.sf.net wrote: [tickets:#67] https://sourceforge.net/p/mocat/tickets/67/ Mocat excedes memory...
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