Entering edit mode
21 months ago
luzglongoria
▴
50
Hi there,
I'm running STAR by using a loop:
time for file in *.fp.fq.gz; do echo ${file%%1.fp.fq.gz}2.fp.fq.gz; STAR --runThreadN 30 --genomeDir /home/path/parasite_index/ --readFilesIn $file ${file%%1.fp.fq.gz}2.fp.fq.gz --readFilesCommand zcat; done
But I get this error:
Dec 01 20:35:37 ..... started STAR run
Dec 01 20:35:37 ..... loading genome
Dec 01 20:35:40 ..... started mapping
Dec 02 20:29:31 ..... finished mapping
Dec 02 20:29:31 ..... finished successfully
R13_2.fp.fq.gz2.fp.fq.gz
EXITING: because of fatal INPUT file error: could not open read file: R13_2.fp.fq.gz2.fp.fq.gz
SOLUTION: check that this file exists and has read permission.
I am running it in the folder where the samples are. The program continues running even with the error (it jumps to the next sample). After a while I get the same error but for another sample. Not all the samples give back an error. Apparently only some of the ones that are "_2" (reverse) not the "_1" (forward).
Here it is the sample specifically. It is in the folder where I'm running the loop.
ls R13_*
R13_1.fp.fq.gz R13_2.fp.fq.gz
Any idea of what's going on? Thank you in advance.
you should use a workflow manager: snakemake, nextflow
see options
-e
,-o pipefail
of bashhow about something like
Thanks Pierre but this loop does not include STAR. What's its point?
debugging.
Look at what will happen with a simple echo.
When it's ok, replace echo with the actual star command.
If I do
Then I get
It seems that all the samples are with their pairs. or?
The point is that your code currently creates variables such as
R13_2.fp.fq.gz2.fp.fq.gz
as part of the loop because you are not parsing it properly. That code suggestion tries to address that.