Open cimendes opened 3 years ago
Hi Inês, apologies for the slow response, I can suggest the following quick fix: add the --no-scaffolding
flag to the gatb
executable. This will skip BESST, and for metagenome paired-end data, this may not be a too bad thing.
Greetings,
I've been using gatb-minima-pipeline for a while now for a de novo assembly software benchmark, available at Github. I've been running it so far without issue with real data, in this case, the ZymoBIOMICS Microbial Community Standard with even and log distribution.
Recently I've generated a mock community with the ZymoBIOMICS complete genomes and GATB-MINIA-PiPELINE is consistently failing on the samples without error model (perfect reads matching the reference). The mock read data is available here
I use the following command to run this assembler:
gatb -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} --kmer-sizes ${kmer_list} -o ${sample_id}_GATBMiniaPipeline --no-error-correction
(available herethe parameters used are
This is the end of the stdout that I get while running gatb-minia-pipeline:
This pipeline is being run in a dockerfile with the latest version in the master branch: cimendes/gatb-minia-pipeline:31.07.2020-1
Thank you for your assistance in understanding this error! Is there anything you suggest I do?
Best,
Inês