MOCAT.cfg not working
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#86 MOCAT.cfg not working
Hello I am having trouble running the basic Mocat.pl pipeline.
I am running this command "MOCAT.pl -sf my.samples -rtf" my sample names are in my.samples and the files are in sub folders. I have attached to you my MOCAt.cfg file.
When I run this command, I get this error
===============================================================================
MOCAT - Metagenomics Analysis Toolkit v2.1.3
by Jens Roat Kultima, Luis Pedro Coelho, Shinichi Sunagawa @ Bork Group, EMBL
===============================================================================
EXECUTE COMMAND : -sf my.samples -rtf
CURRENT USER : ubuntu
CURRENT HOST : kraken
WORKING DIRECTORY : /mnt/volume_3/ICU/patient_list/Patient25
CONFIG FILE : /mnt/volume_3/ICU/patient_list/Patient25/MOCAT.cfg
NUMBER OF SAMPLES : 16
SAMPLE NAMES : 13-6929577, 13-6929578, 13-6929580, 13-6929582, 13-6929583, 13-6929586, 13-6929589, 13-6929891, 13-6929595, 13-6929599, 13-6929600, 13-6929601, 13-6929602, 13-6929604, 13-6929605, 13-6929606
SAMPLE FILE : my.samples
===============================================================================
MOCAT_DEV_DIR : /mnt/volume_3/mocat2/mocat2/stable/2.1.3/
MOCAT_LSF_max_concurrent :
MOCAT_LSF_memory_limit :
MOCAT_LSF_qsub_add_param :
MOCAT_LSF_queue :
MOCAT_PBS_qsub_add_param :
MOCAT_SGE_parallell_env : smp
MOCAT_SGE_qsub_add_param :
MOCAT_SLURM_max_concurrent :
MOCAT_bwa_postprocess_binsize : 500
MOCAT_data_dir : /mnt/volume_3/ICU/patient_list/Patient25
MOCAT_data_type : solexaqa
MOCAT_default_reads : reads.processed
MOCAT_dir : /mnt/volume_3/mocat2/mocat2/stable/2.1.3/
MOCAT_mapping_mode : allbest
MOCAT_paired_end : yes
MOCAT_pre_execute : umask 0002; export LC_ALL=C
MOCAT_prompt_before_run : no
MOCAT_qsub_system : none
MOCAT_record_script_versions : yes
MOCAT_rownames_dir : /mnt/volume_3/ICU/patient_list/Patient25
MOCAT_umask : 0002
MOCAT_zip_level : 9
MOCAT_zip_program : pigz
===============================================================================
ERROR & EXIT: Missing setting 'filter_psort_buffer' in config file. Is the config file correct? at /mnt/volume_3/mocat2/mocat2/stable/2.1.3/src/MOCAT.pl line 637.
When I ran it the first time, I got an error that - "Missing setting 'assembly_revision_scaftig_min_length' in config file"
When I corrected that in the config file, I get this error about filter_psort_buffer.
This is not given in the config file.
Any help on this will be must appreciated!!
Thanks!\
Anu
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:
Related
Tickets: #86
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
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:
Related
Tickets: #86
Last edit: Anuradha Ravi 2018-06-06
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
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:
Related
Tickets: #86