search

linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
130 stars 40 forks source link

dbcan 3 start from raw data,I got some problems with step 13 dbcan_utils to calculate the abundance of CAZyme families, subfamilies, CGCs, and substrates #180

Open powerby66 opened 2 weeks ago

powerby66 commented 2 weeks ago

Report

dbcan_utils fam_abund -bt /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_abund/EscheriaColiK12MG1655.depth.txt -i /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_fna.dbCAN -a TPM dbcan_utils fam_substrate_abund -bt /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_abund/EscheriaColiK12MG1655.depth.txt -i /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_fna.dbCAN -a TPM dbcan_utils CGC_abund -bt /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_abund/EscheriaColiK12MG1655.depth.txt -i /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_fna.dbCAN -a TPM dbcan_utils CGC_substrate_abund -bt /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_abund/EscheriaColiK12MG1655.depth.txt -i /data2/jpc/project/project/db_test/output/EscheriaColiK12MG1655_fna.dbCAN -a TPM This step shows 'dbcan_utils command not found', so I directly imported utils.py, image but there were no results output or error message. What is the correct way to proceed? Thank you!

Version information

No response