Am getting the error below with Velveth. What does the error mean and how can i fix it?
‘’ Fatal error: Exit code 1 ()’’
export OMP_NUM_THREADS="${GALAXY_SLOTS:-1}" && mkdir -p ‘/mnt/tmp/job_working_directory/001/966/1966406/working/dataset_3357803_files’ && velveth ‘/mnt/tmp/job_working_directory/001/966/1966406/working/dataset_3357803_files’ 15 -fastqsanger.gz -shortPaired -interleaved ‘/mnt/user-data/003/357/dataset_3357630.dat’
Hi @walid
Thanks for sending in the bug report as well from the run at UseGalaxy.org.
The root issue is that this is an older tool wrapper that has some special input requirements that differ from current tools. Also, this tool and related tools do not have enough resources allocated to run real analysis – are intended for training purposes only. We’ll be tagging all three tools as deprecated near term at UseGalaxy.org: velvetg, velveth, and VelvetOptimiser. UseGalaxy.eu and UseGalaxy.org.au will continue to tag these tools as “training-only” (at least for now).
Ticket with details
If your local jobs are the same as those reported, if you change the datatype to be “fastq” for the input (uncompress the data first), that may work on your local Galaxy if you allocate enough resources. You may need to test out a few of the “Input type > read type” choices to get a match for the actual input read content and format (single, paired, interleaved pairs – all require a different choice).
Or skip trying to get an older/confusing tool to work, and use SPAdes instead.
Thanks and our apologies for the confusion!