Dietmar Rieder
Dietmar Rieder
Seems to be fixed. Closing it.
Thanks for spotting this, and sorry for the long silence. We will provide a fix in the next release.
Hi, can you provide the contents of `/wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25` as tar.gz file? as well as the `.nextflow.log` Thanks
Unfortunately I cannot see any files.
it seems that the bam files created in teh `pre_map_hla_RNA` are invalid: `/wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/rna_mapped_1.bam` `/wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/rna_mapped_2.bam` what are the contents of that directory?
There seems to be a problem with creating temporary files on your system in the `/scratch` dir: the `.command.err` from the 9e contents says: ``` Couldn't create temporary file /scratch/wwu888/SQN38WCAC....
Hi, it is not `nextNEOpi` directly trying to write into `/scratch/wwu888` it is the `yara_mapper` which reads the ENV variable `$TEMPDIR` and uses that value to write temporary files. I...
Can you provide more details
Closing: no more details provided. Please check if v1.4.1 is fixing this.
Hi, can you post the contents of `/home/ubuntu/nextNEOpi/work/d8/182ae7593f5feda9fa6e7706bd4226/.command.run`