Comments (7)
Sorry, slow reply to this - it's paired reads only
from clockwork.
My guess is that the fastq file(s) were not found or are empty. Does this work?
singularity exec clockwork_container.img ls -lh SAMEA2534421/ERR552113_1.fastq.gz SAMEA2534421/ERR552113_2.fastq.gz
from clockwork.
@martinghunt Thank you for your response but this did not work.
from clockwork.
What was the output?
from clockwork.
(mtb) root@ip:/attach/data/test1# singularity exec clockwork_v0.12.3.img ls -lh SAMEA2534421/ERR552113_1.fastq.gz SAMEA2534421/ERR552113_2.fastq.gz
/usr/bin/ls: cannot access 'SAMEA2534421/ERR552113_1.fastq.gz': No such file or directory
/usr/bin/ls: cannot access 'SAMEA2534421/ERR552113_2.fastq.gz': No such file or directory
(mtb) root@ip:/attach/data/test1# ls SAMEA2534421/
ERR552113_1.fastq.gz ERR552113_2.fastq.gz
from clockwork.
This means your singularity install isn't by default seeing CWD
when you run it. By default it should. The docs are here:
https://docs.sylabs.io/guides/latest/user-guide/bind_paths_and_mounts.html
Could try looking at the examples with --bind
in there? Or setting $SINGULARITY_BIND
to something like /attach/data
?
from clockwork.
@martinghunt It worked out. One quick question , Does this pipeline works on single end fastq input also ?
Many thanks,
Mansi
from clockwork.
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