search

junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
45 stars 16 forks source link

Bowtie problem #37

Closed ceidashi8 closed 9 months ago

ceidashi8 commented 10 months ago

Dear shi,when i can not match to index of bowtie-build，although I already have these index file.The error is that:

match to miRNA-match_genome Could not locate a Bowtie index corresponding to basename "Arabidopsis_thaliana/miRBase_21/miRBase_21-ath" Command: bowtie --wrapper basic-0 -f -v 0 -a -p 1 --fullref --norc --al /home/cuimingyang/sports-sRNA/text/1_S1_1_trimmed/S1_1_trimmed_match_miRNA_match_genome.fa --un /home/cuimingyang/sports-sRNA/text/1_S1_1_trimmed/S1_1_trimmed_unmatch_miRNA_match_genome.fa Arabidopsis_thaliana/miRBase_21/miRBase_21-ath /home/cuimingyang/sports-sRNA/text/1_S1_1_trimmed/S1_1_trimmed_match_genome.fa

junchaoshi commented 9 months ago

Hi, Could you please post the entire command you used when running the SPORTS? It appears that the correct absolute or relative address for the miRBase reference was not entered. I always recommend using the absolute path of the file or folder to avoid any confusion. For instance, the absolute path could be: /home/Genome/Arabidopsis_thaliana/miRBase_21/miRBase_21-ath.

I hope this information is helpful.

Best regards, Junchao

ceidashi8 commented 9 months ago

Thank you,I took your advice to run the Sports successfully!

---Original--- From: @.> Date: Tue, Nov 14, 2023 11:09 AM To: @.>; Cc: @.**@.>; Subject: Re: [junchaoshi/sports1.1] Bowtie problem (Issue #37)

Hi, Could you please post the entire command you used when running the SPORTS? It appears that the correct absolute or relative address for the miRBase reference was not entered. I always recommend using the absolute path of the file or folder to avoid any confusion. For instance, the absolute path could be: /home/Genome/Arabidopsis_thaliana/miRBase_21/miRBase_21-ath.

I hope this information is helpful.

Best regards, Junchao

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>