Closed kittyBS closed 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
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.
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.