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billzt / MiFish

This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
https://mitofish.aori.u-tokyo.ac.jp/mifish/
GNU General Public License v3.0
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Help with multiple input data files (groups) #8

Closed cement-head closed 1 year ago

cement-head commented 1 year ago

The mitofish pipeline is working when I use a single input directory, however, I am trying to analyze the data in three subgroups. I have placed each sub-group into its own folder and specified each of the folders by using the "-d" argument.

However, I am now getting an error (see below) with the pipeline as it seems it cannot find the database.

What am I doing wrong?

$ mifish -o output/WTRBA-YEARS -t 124 -d /home/cbfgws6/MiFish/WTRBA_YEAR/21 -d /home/cbfgws6/MiFish/WTRBA_YEAR/22 -d /home/cbfgws6/MiFish/WTRBA_YEAR/23 /home/cbfgws6/MiFish/mifishdb-Oct2023/mitofish.db.fa
usage: mifish [-h] [-d OTHER_DATA_DIR] [-m MIN_READ_LEN] [-M MAX_READ_LEN] [-f PRIMER_FWD] [-r PRIMER_REV] [-u UNOISE_MIN] [-i BLAST_MIN_IDENTITY] [-s] [-k]
              [-o OUTPUT_DIR] [-t THREADS]
              seq_dir db
mifish: error: the following arguments are required: db
cement-head commented 1 year ago

Whoops! I figured it out. In the instructions the fact that the seq file is called seq confused me.

Here's the command that worked: $ mifish /home/cbfgws6/MiFish/WTRBA_YEAR/21 /home/cbfgws6/MiFish/mifishdb-Oct2023/mitofish.db.fa -d /home/cbfgws6/MiFish/WTRBA_YEAR/22 -d /home/cbfgws6/MiFish/WTRBA_YEAR/23-o output/WTRBA-YEARS -t 124

billzt commented 1 year ago

I have added a note in the README file.