PUL annotation question

[LuckyFeiX]

Dear Developers,

This software is helpful, but its new V4 parameters are too complex. I want to know the PUL in my genome, but I don't know if the following shell is right. I can run it but cannot find the result about PUL.

run_dbcan bin.13.faa protein -c bin.13.gff --dia_cpu 25 --hmm_cpu 25 --tf_cpu 25 --stp_cpu 25 --out_pre bin.13 --out_dir bin.13 --use_signalP=TRUE -sp /mnt/sdb/software/interproscan-5.57-90.0/bin/signalp/4.1/signalp --db_dir /mnt/sdb/database/cazydb/db/ --pul /mnt/sdb/database/cazydb/db/PUL.faa

Could you tell me which file I should see the results in? Or tell me how to modify the parameters. Thank you~

[zhengzhengzhj]

Dear user, The basic command to get the PUL and their potential substrate is "run_dbcan EscheriaColiK12MG1655.fna meta --out_dir samples --cluster 1 --cgc_substrate". If all the databases are in the "db" folder of the working directory. You will find all the result files in "samples" folder.

For your specific inputs, you can use this command: "run_dbcan bin.13.faa protein -c bin.13.gff --dia_cpu 25 --hmm_cpu 25 --tf_cpu 25 --stp_cpu 25 --out_pre bin.13 --out_dir bin.13 --use_signalP=TRUE -sp /mnt/sdb/software/interproscan-5.57-90.0/bin/signalp/4.1/signalp --db_dir /mnt/sdb/database/cazydb/db/ --cgc_substrate " option --cgc_substrate will enable predicting substrate for all the potential PUL predicted by cgc_finder.

[yinlabniu]

The substrate prediction is in sub.prediction.out.

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From: zhengzhengzhj @.> Sent: Sunday, April 23, 2023 7:19 PM To: linnabrown/run_dbcan @.> Cc: Subscribed @.***> Subject: Re: [linnabrown/run_dbcan] PUL annotation question (Issue #116)

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Dear user, The basic command to get the PUL and their potential substrate is "run_dbcan EscheriaColiK12MG1655.fna meta --out_dir samples --cluster 1 --cgc_substrate". If all the databases are in the "db" folder of the working directory. You will find all the result files in "samples" folder.

For your specific inputs, you can use this command: "run_dbcan bin.13.faa protein -c bin.13.gff --dia_cpu 25 --hmm_cpu 25 --tf_cpu 25 --stp_cpu 25 --out_pre bin.13 --out_dir bin.13 --use_signalP=TRUE -sp /mnt/sdb/software/interproscan-5.57-90.0/bin/signalp/4.1/signalp --db_dir /mnt/sdb/database/cazydb/db/ --cgc_substrate " option --cgc_substrate will enable predicting substrate for all the potential PUL predicted by cgc_finder.

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