search

Gabaldonlab / redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
GNU General Public License v3.0
129 stars 20 forks source link

OSError: [Errno 17] File exists #75

Closed Kata-Pa closed 4 years ago

Kata-Pa commented 4 years ago

Hello!

I ve been running Redundans in the past several times with no problem (with the only difference of using --noscaffolding), but suddenly now I get an error (even if I add noscaffolding parameter). Here is my command: redundans.py -f ../flye/assembly.fasta -i ../../My_Illumina/Trimmed/Cylindro.Illumina.fwd.Gold.5.20.paired.fastq ../../My_Illumina/Trimmed/Cylindro.Illumina.rv.Gold.5.20.paired.fastq ../../My_Illumina/Trimmed/Cylindro.IlluminaRun2.fwd.Gold.5.20.paired.fastq ../../My_Illumina/Trimmed/Cylindro.IlluminaRun2.rv.Gold.5.20.paired.fastq -l ../All_Minion.fastq --log MaSuRCa_Redund -o MaSuRCa_Redund

And the error I get is: Traceback (most recent call last): File "/home/katerina87/Tools/redundans/redundans.py", line 541, in main() File "/home/katerina87/Tools/redundans/redundans.py", line 536, in main o.norearrangements, o.verbose, o.usebwa, o.log, o.tmp) File "/home/katerina87/Tools/redundans/redundans.py", line 289, in redundans os.makedirs(outdir) File "/usr/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 17] File exists: 'MaSuRCA_Redund'

Even though the output file does not exist when I run the command. I am using python 2.7 and I tried in two different servers,I got the same error. Any hint on what is wrong?

Thank you! /Katerina

Kata-Pa commented 4 years ago

Ok, no need to reply here (though I guess noone was going to), I solved it myself. Avoid using the same name for log and output, as this creates the file exists error.