Issue with Diamond

[fchiesa]

When running the script I get this message:

step2:identify phage or phage-like genes
DBSCAN-SWA/software/diamond/diamond blastp -d DBSCAN-SWA/db/database/uniprot.dmnd -q prova/protein_annotation/listeria_protein.faa -f 6 -e 1e-07 -o prova/phage_gene_cluster/listeria_blastp_uniprot.txt -p 20 --max-target-seqs 1
sh: 1: DBSCAN-SWA/software/diamond/diamond: Permission denied

It obviously ends with "No phage or phage-like gene was identified in the query genome!", since is not using diamond.
I wanted to change path to the diamond installed by conda, but I'm not skilled enough.
Do you have any clue?
Thank you in advance

[HIT-ImmunologyLab]

Please grant permission to run diamond, you can perform the follwing command: chmod a+x -R DBSCAN-SWA/software I suggest you use the diamond given by DBSCAN-SWA in case of unmatch with the pre-built diamond database

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-----原始邮件----- 发件人:fchiesa <[email protected]> 发送时间:2020-12-01 04:45:46 (星期二) 收件人: HIT-ImmunologyLab/DBSCAN-SWA <[email protected]> 抄送: Subscribed <[email protected]> 主题: [HIT-ImmunologyLab/DBSCAN-SWA] Issue with Diamond (#2) When running the script I get this message: step2:identify phage or phage-like genes DBSCAN-SWA/software/diamond/diamond blastp -d DBSCAN-SWA/db/database/uniprot.dmnd -q prova/protein_annotation/listeria_protein.faa -f 6 -e 1e-07 -o prova/phage_gene_cluster/listeria_blastp_uniprot.txt -p 20 --max-target-seqs 1 sh: 1: DBSCAN-SWA/software/diamond/diamond: Permission denied It obviously ends with "No phage or phage-like gene was identified in the query genome!", since is not using diamond. I wanted to change path to the diamond installed by conda, but I'm not skilled enough. Do you have any clue? Thank you in advance — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.