i am currently running the rnaseq module and it gets frozen [9a/8a331f] NFC…PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa) [ 0%] 0 of 1 i am not sure whether i am using the correct fasta and gft files

The files look fine to me (I would be using those), and either way, even "wrong" ones should not cause any "freezing", if that's indeed what is happening. How long has it been in that state? Where are you running this, and with what configuration? This is not a common problem, so I would start by looking in the server/node/VM where this process is running if either

samtools

or

cut

is running there (in a container?), and if it is actually doing something. For the first part of the question

pgrep

is useful, for the second part you could look at CPU usage with something like

htop

or

top

, or you could see if files are being created in the work directory of the process (you can find that if you look for

CUSTOM_GETCHROMSIZES

and [in this case]

9a/8a331f

in the

.nextflow.log

file in the directory where you started the pipeline). BTW, if you have any questions specific to the rnaseq pipeline, there is a specialized channel #CE8SSJV3N.