Error running this command: fqtools count about clockwork HOT 7 CLOSED

Sorry, slow reply to this - it's paired reads only

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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

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@martinghunt Thank you for your response but this did not work.

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What was the output?

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@martinghunt

(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

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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?

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@martinghunt It worked out. One quick question , Does this pipeline works on single end fastq input also ?

Many thanks,
Mansi

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