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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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Output folder #39

Closed kittyBS closed 7 months ago

kittyBS commented 7 months ago

Hi! I started the analysis twice using the code below. The analysis was completed without any problems the first time. On my second try, I changed the files in seq_address.txt and ran it again, but I got the following error. "Command: bowtie-build --wrapper basic-0 --threads 24 -q /home/yildize/sports/Mus_musculus/genome/mm10/genome.fa /home/yildize/sports/Mus_musculus/genome/mm10/genome mv: cannot stat '/home/yildize/sports/output/sh_file/.sh': No such file or directory rmdir: failed to remove '/home/yildize/sports/output/sh_file': No such file or directory rm: cannot remove '/home/yildize/sports/output/.sh': No such file or directory" The code I used in both analyzes is;"sports.pl -i seq_address.txt -p 24 -g /home/yildize/sports/Mus_musculus/genome/mm10/genome -m /home/yildize/sports/Mus_musculus/miRBase/21/miRBase_21-mmu -r /home/yildize/sports/Mus_musculus/rRNAdb/mouse_rRNA -t /home/yildize/sports/Mus_musculus/GtRNAdb/mm10/mm10-tRNAs -w /home/yildize/sports/Mus_musculus/piRBase/piR_mouse -f /home/yildize/sports/Mus_musculus/Rfam/12.3/Rfam-12.3-mouse -o /home/yildize/sports/untroutput/" Thank you in advance for your time.

junchaoshi commented 7 months ago

Hi,

It seems there's an issue with the bowtie index building procedure. Could you check the mouse fgenome reference folder?

Junchao

kittyBS commented 7 months ago

Thank you for your return. Unfortunately, deleting the reference genome and reinstalling did not solve the problem. When I deleted and reinstalled the tool, the problem seems to be solved. Analysis is currently running.