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keylabivdc / VIP

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Problems with path #3

Closed IgorFobia closed 8 years ago

IgorFobia commented 8 years ago

I run your script with the following command /opt/VIP/VIP.sh -c EUV01121_unmapped_f5_1.fastq.conf -i EUV01121_unmapped_f5_1.fastq

from directory /home/fgori/Validation/XXX/unmapped_reads/

I get the following errors, and other similar errors: usr/VIP/bin/covplot.sh: line 41: temp./home/fgori/Validation/XXX/unmapped_reads/EUV01121_unmapped_f5_1.fastq.nohost.nobac.sense_nucl.match.sam.addseq.VIRUSES.all.annotated.nospace:

Therefore, it seems that the lines generating temporary file paths are buggy.

keylabivdc commented 8 years ago

Hi,

It looks like the path of the file was added into the command line. Please do not include any path information. That is to say, please use VIP.sh -i file instead of VIP.sh -i [PATH]/file ***.

IgorFobia commented 8 years ago

Thanks. Honestly, it would be much better if VIP would not required to be called in the folder where he file is contained.