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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Adding plasmid sequences error #77

Closed pavlo888 closed 3 years ago

pavlo888 commented 3 years ago

Hi,

I am trying to add a set of plasmids to the current plasmid db of mob-suite. However I am not being successful at it.

I am running this command:

mob_cluster --mode update -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonomy.txt --outdir output_directory -c existing_clusters.txt -r existing_sequences.fasta

And I am getting this error:

2020-12-08 20:50:05,704 root INFO: Running Mob-Suite Clustering toolkit v. 3.0.0 [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/mob_cluster.py:451] 2020-12-08 20:50:05,704 root INFO: Processing fasta file new_plasmids.fasta [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/mob_cluster.py:452] 2020-12-08 20:50:05,704 root INFO: Analysis directory output_directory [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/mob_cluster.py:453] 2020-12-08 20:50:05,704 root INFO: SUCCESS: Found program blastn at /home/sam/anaconda3/envs/mobsuite/bin/blastn [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/utils.py:571] 2020-12-08 20:50:05,704 root INFO: SUCCESS: Found program makeblastdb at /home/sam/anaconda3/envs/mobsuite/bin/makeblastdb [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/utils.py:571] 2020-12-08 20:50:05,704 root INFO: SUCCESS: Found program tblastn at /home/sam/anaconda3/envs/mobsuite/bin/tblastn [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/utils.py:571] 2020-12-08 20:50:05,704 root ERROR: Error, input metadata file specified does not exist: new_plasmids_mobtyper_report.txt [in /home/sam/anaconda3/envs/mobsuite/lib/python3.6/site-packages/mob_suite-3.0.1-py3.6.egg/mob_suite/mob_cluster.py:464]

Could you help me solve this issue?

Thanks!

jrober84 commented 3 years ago

The error code from the tool is saying that your metadata file new_plasmids_mobtyper_report.txt does not exist. You will need to provide the tool with the full path to each of the required files if the file is not in your current directory.