search

Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
Other
38 stars 15 forks source link

Caution: long input filenames create unrelated error messages #26

Closed markb729 closed 5 years ago

markb729 commented 5 years ago

Hi Elizabeth,

When using sqanti_qc2.py, if the filename of the input fasta file is sufficiently long (and possibly including the path too), GeneMark will throw an error.

Error on open output file /mnt/data/IsoSeq_20190729/GMST/GMST_tmp GeneMarkS: error on last system call, error code 256 Abort program!!!

Examination of the GeneMark log file suggests that gmst.pl is happy, but probuild is not:

/mnt/data/IsoSeq_20190729/SQANTI2/utilities/gmst/probuild --par /mnt/data/IsoSeq_20190729/SQANTI2/utilities/gmst/par_1.default --clean_join sequence --seq /mnt/data/IsoSeq_20190729/m54178_190723_19024 0.ccs.demux.primer_5p--primer_3p_flnc_polished_CUPCAKE.collapsed.rep.renamed_corrected.fasta --log gms.log Error on last system call, error code 256 Abort program!!!

Direct invocation of probuild yields the following uninformative error:

error in command line

This feature is clearly related to GeneMark and not SQANTI2. Nevertheless, keeping the length of input filenames to a minimum solves this issue.

Sincerely, Mark

Magdoll commented 5 years ago

Hi @markb729 , How long was your filename?

markb729 commented 5 years ago

I have not tested the minimum number required to throw an error, but 94 characters without the path (or 136 with the path) will cause the error.

anilkanthi commented 4 years ago

Hi @markb729 This was helpful! Wouldn't have thought the errors were due to the filename length.. @Magdoll Would it be possible to fix this as even the most recent version faced the issue? Thank you.