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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
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hostrange() missing 1 required positional argument: 'database_directory' #148

Closed rpetit3 closed 1 year ago

rpetit3 commented 1 year ago

Hello!

Ran into the following issue:

2023-08-11 16:48:51,834 mob_suite.mob_recon INFO: MOB-recon version 3.1.5  [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:980]
2023-08-11 16:48:51,834 mob_suite.mob_recon INFO: SUCCESS: Found program blastn at /usr/local/bin/blastn [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:592]
2023-08-11 16:48:51,834 mob_suite.mob_recon INFO: SUCCESS: Found program makeblastdb at /usr/local/bin/makeblastdb [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:592]
2023-08-11 16:48:51,835 mob_suite.mob_recon INFO: SUCCESS: Found program tblastn at /usr/local/bin/tblastn [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:592]
2023-08-11 16:48:51,835 mob_suite.mob_recon INFO: Processing fasta file GCF_000017085.fna [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1007]
2023-08-11 16:48:51,835 mob_suite.mob_recon INFO: Analysis directory results [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1008]
2023-08-11 16:48:58,964 mob_suite.mob_recon INFO: Writing cleaned header input fasta file from GCF_000017085.fna to results/__tmp/fixed.input.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1103]
2023-08-11 16:48:59,606 root INFO: Blasting replicon sequences /usr/local/lib/python3.8/site-packages/mob_suite/databases/rep.dna.fas against results/__tmp/fixed.input.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1150]
2023-08-11 16:49:00,609 root INFO: Filtering replicon blast results results/__tmp/replicon_blast_results.txt  [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1155]
2023-08-11 16:49:00,637 root INFO: Blasting relaxase sequences /usr/local/lib/python3.8/site-packages/mob_suite/databases/mob.proteins.faa against results/__tmp/fixed.input.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1173]
2023-08-11 16:49:29,561 root INFO: Filtering relaxase blast results results/__tmp/mob_blast_results.txt  [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1178]
2023-08-11 16:49:29,577 root INFO: Blasting MPF sequences /usr/local/lib/python3.8/site-packages/mob_suite/databases/mpf.proteins.faa against results/__tmp/fixed.input.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1197]
2023-08-11 16:49:53,027 root INFO: Filtering MPF blast results results/__tmp/mpf_blast_results.txt  [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1212]
2023-08-11 16:49:53,028 root INFO: Blasting orit sequences /usr/local/lib/python3.8/site-packages/mob_suite/databases/orit.fas against results/__tmp/fixed.input.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1221]
2023-08-11 16:49:53,230 root INFO: Filtering orit blast results results/__tmp/orit_blast_results.txt  [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1226]
2023-08-11 16:49:53,254 root INFO: Blasting contigs against repetitive sequences db: /usr/local/lib/python3.8/site-packages/mob_suite/databases/repetitive.dna.fas [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1243]
2023-08-11 16:49:53,909 root INFO: Filtering repetitive blast results results/__tmp/repetitive_blast_results.txt  [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:1247]
2023-08-11 16:49:53,916 root INFO: Blasting contigs against reference sequence db: /usr/local/lib/python3.8/site-packages/mob_suite/databases/ncbi_plasmid_full_seqs.fas [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1260]
2023-08-11 16:50:00,642 root INFO: Filtering contig blast results: results/__tmp/contig_blast_results.txt [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1265]
2023-08-11 16:50:00,795 root INFO: Assigning contigs to plasmid groups [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1280]
2023-08-11 16:50:03,017 root INFO: b"mash: Relink `/usr/local/bin/../lib/./libgfortran.so.5' with `/lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'\n" [in /usr/local/lib/python3.8/site-packages/mob_suite/wrappers/__init__.py:23]
2023-08-11 16:50:03,623 root INFO: b"mash: Relink `/usr/local/bin/../lib/./libgfortran.so.5' with `/lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'\n" [in /usr/local/lib/python3.8/site-packages/mob_suite/wrappers/__init__.py:23]
2023-08-11 16:50:03,652 root INFO: Writting contig results to results/contig_report.txt [in /usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py:1382]
2023-08-11 16:50:08,510 root INFO: Writting plasmid sequences to results/plasmid_AA840.fasta [in /usr/local/lib/python3.8/site-packages/mob_suite/utils.py:957]
Traceback (most recent call last):
  File "/usr/local/bin/mob_recon", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/site-packages/mob_suite/mob_recon.py", line 1395, in main
    build_mobtyper_report(contig_memberships['plasmid'], out_dir, mobtyper_report,contig_seqs, ncbi, lit,ETE3DBTAXAFILE)
  File "/usr/local/lib/python3.8/site-packages/mob_suite/utils.py", line 1067, in build_mobtyper_report
    host_range = hostrange(rep_types, relaxase_types, mob_cluster_id, ncbi, lit,ETE3DBTAXAFILE)
TypeError: hostrange() missing 1 required positional argument: 'database_directory'

Command used:

mob_recon \
    --infile GCF_000017085.fna \
    --max_contig_size 310000 --min_length 1000 --max_plasmid_size 350000 \
    --num_threads 4 \
    --outdir results \
    --sample_id GCF_000017085

This was using the Singularity image here: https://depot.galaxyproject.org/singularity/mob_suite:3.1.5--pyhdfd78af_0

The input fasta, GCF_000017085.fna is available here: https://github.com/bactopia/bactopia-tests/blob/main/data/species/staphylococcus_aureus/genome/GCF_000017085.fna

I was able to replicate this on Docker (quay.io/biocontainers/mob_suite:3.1.5--pyhdfd78af_0) and Conda.

I think https://github.com/phac-nml/mob-suite/pull/149 should fix the issue

jrober84 commented 1 year ago

Thanks so much for your help @rpetit3, it is really appreciated! Your PR has been incorporated and a new release 3.1.6 issued to fix the problem.