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Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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Existing files from "incomplete" runs cause errors on subsequent runs #49

Closed wolfgangrumpf closed 4 years ago

wolfgangrumpf commented 4 years ago

I'm in the middle of prepping a script to perform this analysis, and I'd forgotten to enable the gmap module on my system - so sqanti kind of ran but didn't. Subsequently, it continued to fail until I deleted the files that were created during the aborted attempt - apparently it doesn't like having pre-existing files:

**** Predicting ORF sequences... terminate called after throwing an instance of 'std::length_error' what(): basic_string::_S_create GeneMarkS: error on last system call, error code 134 Abort program!!! Traceback (most recent call last): File "/opt/sqanti2/4.1/SQANTI2-4.1/sqanti_qc2.py", line 1793, in main() File "/opt/sqanti2/4.1/SQANTI2-4.1/sqanti_qc2.py", line 1789, in main run(args) File "/opt/sqanti2/4.1/SQANTI2-4.1/sqanti_qc2.py", line 1414, in run orfDict = correctionPlusORFpred(args, genome_dict) File "/opt/sqanti2/4.1/SQANTI2-4.1/sqanti_qc2.py", line 555, in correctionPlusORFpred if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0: File "/opt/sqanti2/4.1/anaCogent3/lib/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'perl /gpfs0/export/opt/sqanti2/4.1/SQANTI2-4.1/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /gpfs0/home/gdlauberlab/rwr002/TESTING/ISOSEQ_2/GMST/GMST_tmp /gpfs0/home/gdlauberlab/rwr002/TESTING/ISOSEQ_2/cupcake.gmap.collapsed.rep.renamed_corrected.fasta' returned non-zero exit status 1

Magdoll commented 4 years ago

HI @wolfgangrumpf , Yes you need to clean up the old - half failed directories. That said, SQANTI2 was designed to re-use existing files, often because this will save time, esp in regards to ORF prediction.

-Liz