missing output files?

[xvazquezc]

Hi again, I got to complete my test run with the dataset from one of my replicate samples but based on the description of the outputs from the graft option in the wiki, the following files are missing:

• command_log.txt
• my_reads_coverage_table.txt
• my_reads_relative_table.txt
• my_reads_placements.guppy

Any idea why? The job got completed in the cluster with no error message:

02/12/2016 04:23:03 PM INFO: Working on 028-LFA_S1_R1 02/12/2016 04:23:03 PM INFO: Working on forward reads 02/12/2016 04:41:15 PM INFO: Found 573 read(s) that may be eukaryotic 02/12/2016 04:42:11 PM INFO: 10659 read(s) detected 02/12/2016 04:42:11 PM INFO: aligning reads to reference package database 02/12/2016 04:45:07 PM INFO: Filtered 1788 short sequences from the alignment 02/12/2016 04:45:07 PM INFO: 8871 sequences remaining 02/12/2016 04:45:07 PM INFO: Working on reverse reads 02/12/2016 05:03:18 PM INFO: Found 576 read(s) that may be eukaryotic 02/12/2016 05:04:13 PM INFO: 10606 read(s) detected 02/12/2016 05:04:13 PM INFO: aligning reads to reference package database 02/12/2016 05:07:04 PM INFO: Filtered 1782 short sequences from the alignment 02/12/2016 05:07:04 PM INFO: 8824 sequences remaining 02/12/2016 05:07:05 PM INFO: Placing reads into phylogenetic tree 02/13/2016 09:10:38 AM INFO: Placements finished 02/13/2016 09:10:44 AM INFO: Reading classifications 02/13/2016 09:10:45 AM INFO: Reads classified 02/13/2016 09:10:50 AM INFO: 6463 reads found that crossover in 028-LFA_S1_R1_forward_clustered.fa 02/13/2016 09:12:02 AM INFO: Writing summary table 02/13/2016 09:12:02 AM INFO: Writing biom file 02/13/2016 09:12:02 AM INFO: Building summary krona plot 02/13/2016 09:12:03 AM INFO: Cleaning up 02/13/2016 09:12:03 AM INFO: Done, thanks for using graftM!

                         GraftM 0.9.4

                            GRAFT

                   Joel Boyd, Ben Woodcroft

                                                     __/__
                                              ______|
      _- - _                         ________|      |_____/
       - -            -             |        |____/_
       - _     >>>>  -   >>>>   ____|
      - _-  -         -             |      ______
         - _                        |_____|
       -                                  |______

Job resources allocated:

#PBS -l nodes=12:ppn=1
#PBS -l vmem=450gb
#PBS -l walltime=100:00:00

Job command:

graftM graft --forward high_quality_genomes/028-LFA_S1_R1.fastq --reverse high_quality_genomes/028-LFA_S1_R2.fastq --force \
--graftm_package ~/bin/mypythondir/mypythonenv/mypythonenv/share/4.05.2013_08_greengenes_97_otus.gpkg \
--output_directory graftm --threads 12 --input_sequence_type nucleotide --euk_check

Job completion message

Exec host: kc05b11/2+kc05b11/1+kc05b11/0+kc05b12/12+kc05b14/12+kc05b16/4+kc05b16/0+kc09b16/0+kc08b03/3+kc08b03/2+kc08b04/2+kc08b04/1 Execution terminated Exit_status=0 resources_used.cput=47:39:10 resources_used.mem=429466580kb resources_used.vmem=429998872kb resources_used.walltime=16:49:14

[geronimp]

Hello Xabier,

That would be because I've neglected to update the wiki page with some recent updates we've made to GraftM - I apologise for this!

I'll work on updating that as soon as possible, thank you for flagging this for me

I notice also that you are running GraftM with the same directory being passed to the --output_directory flag as the previous issue you raised (https://github.com/geronimp/graftM/issues/182). I'll note that run creates a new output directory, and if the --force flag is used, the previous run is overwritten. Please be careful that if you plan to do multiple runs of graftM runs in the same directory, make sure to give the output directories for each a unique name.

If you have any more bug reports, please keep posting them.

Joel

[geronimp]

Updates have been posted.