I am using trinity and the error message is:
"Fatal error: Exit code 1 ()
cp: -r not specified; omitting directory ‘trinity_out_dir/Trinity.tmp.fasta.salmon.idx’
/ocean/projects/mcb140028p/xcgalaxy/main/staging/50922182/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/50922182/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory"
I don’t understand what is the problem here. The fastq files are OK and there are “1” and “2” in the names of sequences.
That type of stdout error can include problems with read content. There is much QA at this forum about common solutions. Please give that a review first, and if you are stuck later, share back more details and we can try to help more.
This post from yesterday lists out the exact information we will need to help you as well. The stderr at a minimum, a copy/paste of the full job information page report if the stderr also does not include any meaningful information. Make sure all input datasets and both logs are expanded, or we will need to ask you for that again. An error occurred when I used Trinity to analysis my RNA-seq data (clean paired-end fq.gz files) - #4 by jennaj
Let’s start there, thanks!