Closed Zinksulfid closed 3 years ago
Hi @Florian,
Thanks a lot for pointing that out and apologies for getting back to you this late. I tested it on a platform with Centos OS & Bourne shell but did not manage to reproduce the error. So I wonder this could be OS/Shell specific. Can you give me more details about your OS and shell? Thanks a lot.
Wrong @ mention :)
Hello,
when I run Epinano_Current.sh in genome mode with
.../Epinano_Current.sh -b .../file2.sorted.bam -r .../file.fastq -f .../file.fasta -d fast5_folder -t 8 -m g
I get the following error:usage: create a table containing current intensity and duration information in 5mer windows [-h] --intensity_table INTENSITY_TABLE [--window WINDOW] create a table containing current intensity and duration information in 5mer windows: error: unrecognized arguments: _events.collapsed/Intensity.collapsed.tsv
Could it be that there are two spaces too much in Epinano_Current.sh in line 64 and 65, in which
python ${src_d}/misc/Slide_Intensity.py --intensity_table ${evaln}.reverse _events.collapsed/Intensity.collapsed.tsv --window 5
should rather be... reverse_events.collapsed/Intensity.collapsed.tsv ...
and the same for the reverse strand events in l. 65?This did solve the issue for me I suppose, maybe others will profit as well. Thank you for this amazing tool and the valuable documentation!
/Florian