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sunzhengCDNM / MAP2B

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error during run #1

Open sudeep71 opened 9 months ago

sudeep71 commented 9 months ago

Hi

I was planning to use this pipeline but have run into some problems. Could you help?

Command: python3 bin/MAP2B_comment.py -i example/data/data.list -o trial -d /MAP2B/database/GTDB -p 4 -g 5

I have installed and downloaded the GTDB/Refseq databases in the install step. When i follow the example file, it starts by reinstalling the databases. which i think is not needed. I took care of this by commenting out the few lines that install the process. Now it runs but then throws an error

2024-02-15 16:47:24 - CalculateRelativeAbundance_Single2bEnzyme.py - ERROR - file does not exist: path to/GTDB/GTDB/abfh_classify_with_speciename.txt.gz

Now if you look at error it has made a second folder GTDB with the GTDB folder. I do have the "abfh_classify_with_speciename.txt.gz" in the original folder.

Thanks!

sunzhengCDNM commented 8 months ago

Hi,

Thanks for the question.

For parameter -d, you only need to assign a file path to it without any specific database (so the correct command is python3 bin/MAP2B_comment.py -i example/data/data.list -o trial -d /MAP2B/database -p 4 -g 5).

Hope it helps.

Best, Zheng As for choosing GTDB or RefSeq, the parameter is -s [GTDB/RefSeq].

sudeep71 @.***> 于2024年2月16日周五 14:59写道：

Hi

I was planning to use this pipeline but have run into some problems. Could you help?

Command: python3 bin/MAP2B_comment.py -i example/data/data.list -o trial -d /MAP2B/database/GTDB -p 4 -g 5

I have installed and downloaded the GTDB/Refseq databases in the install step. When i follow the example file, it starts by reinstalling the databases. which i think is not needed. I took care of this by commenting out the few lines that install the process. Now it runs but then throws an error

2024-02-15 16:47:24 - CalculateRelativeAbundance_Single2bEnzyme.py - ERROR

  • file does not exist: path to/GTDB/GTDB/abfh_classify_with_speciename.txt.gz

Now if you look at error it has made a second folder GTDB with the GTDB folder. I do have the "abfh_classify_with_speciename.txt.gz" in the original folder.

Thanks!

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sudeep71 commented 8 months ago

Thanks let me give it a try.