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langmead-lab / monorail-external

examples to run monorail externally
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run_recount_unify.sh ERROR: --acc-col of 1 is larger than number of fields #11

Closed dfermin closed 2 years ago

dfermin commented 2 years ago

Hello.

I was able to successfully run the run_recount_pump.sh script with your help on the earlier post. (Thank you for that).

My new problem is with the run_recount_unify.sh.

I have my pump output in: /nfs/md1/RECOUNT3/output. There are 3 samples in there:

/nfs/md1/RECOUNT3/output/X24951431_att0
/nfs/md1/RECOUNT3/output/X24951432_att0
/nfs/md1/RECOUNT3/output/X24951433_att0

My sample_metadata.tsv file looks like this:

study_id    sample_id
testM   X24951431
testM   X24951432
testM   X24951433

(Although the data looks like it's space-delimited here it's actually tab-delimited as required)

When I run the run_recount_unify.sh script the end of the STDOUT is:

Sample ID manifest: /container-mounts/working/ids.input
+ test -n /container-mounts/working/ids.input
+ test -e /container-mounts/working/ids.input
++ head -1 /container-mounts/working/ids.input
++ tr '\t' '\n'
++ wc -l
+ num_cols=2
+ [[ -z '' ]]
+ [[ 2 -ne 3 ]]
+ [[ 2 -ne 2 ]]
+ pushd /recount-unify/sample_ids
/recount-unify/sample_ids /container-mounts/working ~
+ /usr/bin/python2.7 assign_compilation_ids.py --accessions-file /container-mounts/working/ids.input --acc-col 1 --compilation-code 101 --no-header

This is it and the output files don't see to get created. I looked in the unifier/assign_compilation_ids.py.errs file for a clue and this is the error I see:

ERROR: --acc-col of 1 is larger than number of fields in /container-mounts/working/ids.input, terminating!

Any suggestions on what I might be doing wrong?

I'm using the 1.0.9 version of the unify singularity image if that helps.

Thanks,

dfermin commented 2 years ago

Figured it out. An extra blank line was present in the sample_metadata.tsv file causing the error.