Runs with test data do not result in hits - apparently error loading shared libraries

[pdy1084]

Hello,

Recently I run mob_typer with all the tests datasets provided in the Tests/ folder but I could not detect any hit.

I set up a conda environment using conda create -n mob_suite mob_suite pandas==1.0.0 conda-forge::biopython (as reported in #169 (comment) by me). With the installation I could run Mob_recon without problems but for the Mob_typer I only obtain the headers, no hits.

So I went to the folder TestData/ in the conda environment path for the mob_suite and merged all the fasta inputs cat *fasta > merged_input.fasta.

Then I simply run
mob_typer --multi --infile merged_input.fasta --out_file sample_mobtyper_gene_test.txt --mge_report_file mobtyper_report_test.txt

Once it finished I checked the output and the report and both are empty, only the headers.

The output from the console is the following:

(mob_suite) skylake pdy23@l41:/mob_suite/tests/TestData$ mob_typer --multi --infile merged_input.fasta --out_file sample_mobtyper_gene_test.txt --mge_report_file mobtyper_report_test.txt
2024-10-23 16:07:37,068 mob_suite.mob_typer INFO: Running Mob-typer version 3.1.9 [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:172]
2024-10-23 16:07:37,068 mob_suite.mob_typer INFO: Processing fasta file merged_input.fasta [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:174]
2024-10-23 16:07:37,069 mob_suite.mob_typer INFO: Creating analysis directory Trash/tmpxdp6z6og [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:187]
2024-10-23 16:07:37,070 mob_suite.mob_typer INFO: SUCCESS: Found program blastn at .conda/envs/mob_suite/bin/blastn [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:597]
2024-10-23 16:07:37,070 mob_suite.mob_typer INFO: SUCCESS: Found program makeblastdb at .conda/envs/mob_suite/bin/makeblastdb [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:597]
2024-10-23 16:07:37,071 mob_suite.mob_typer INFO: SUCCESS: Found program tblastn at .conda/envs/mob_suite/bin/tblastn [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:597]
2024-10-23 16:07:37,071 mob_suite.mob_typer INFO: Warning! Needed database missing ".conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/ncbi_plasmid_full_seqs.fas.msh" [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:324]
2024-10-23 16:07:37,072 mob_suite.utils INFO: Database directory folder already exists at
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:133]
2024-10-23 16:07:37,072 mob_suite.utils INFO: Placed lock file at .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/.lock [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:145]
2024-10-23 16:07:37,072 mob_suite.utils INFO: Initializing databases...this will take some time [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:168]
2024-10-23 16:07:37,072 mob_suite.utils INFO: Downloading databases...this will take some
time [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:188]
2024-10-23 16:07:37,072 mob_suite.utils INFO: Trying mirror https://zenodo.org/records/10304948/files/data.tar.gz?download=1 [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:192]
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 450M 100 450M 0 0 140M 0 0:00:03 0:00:03 --:--:-- 140M
2024-10-23 16:07:40,278 mob_suite.utils INFO: Downloading databases successful, now building databases at .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:201]
2024-10-23 16:07:40,278 mob_suite.utils INFO: Decompressing .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/data.tar.gz [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:107]
2024-10-23 16:07:53,448 mob_suite.utils INFO: Building repetitive mask database [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:214]
2024-10-23 16:07:53,690 mob_suite.utils INFO: Building complete plasmid database [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:218]
2024-10-23 16:08:10,611 mob_suite.utils INFO: Sketching complete plasmid database [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:222]
2024-10-23 16:08:10,616 mob_suite.utils INFO: Init ete3 library ... [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:234]
2024-10-23 16:08:10,618 mob_suite.utils INFO: MOB init completed successfully [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_init.py:258]
2024-10-23 16:08:13,222 root INFO: Blasting replicon sequences .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/rep.dna.fas against Trash/tmpxdp6z6og/fixed.input.fasta [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1163]
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:338: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
2024-10-23 16:08:13,993 root INFO: Filtering replicon blast results Trash/tmpxdp6z6og/replicon_blast_results.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1168]
2024-10-23 16:08:14,073 root INFO: Blasting relaxase sequences .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/mob.proteins.faa against Trash/tmpxdp6z6og/fixed.input.fasta [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1186]
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:365: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
2024-10-23 16:08:27,980 root INFO: Filtering relaxase blast results Trash/tmpxdp6z6og/mobtyper_blast_results.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1191]
2024-10-23 16:08:28,009 root INFO: Blasting MPF sequences .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/mpf.proteins.faa against Trash/tmpxdp6z6og/fixed.input.fasta [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1210]
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:365: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
2024-10-23 16:08:38,565 root INFO: Filtering MPF blast results Trash/tmpxdp6z6og/mpf_blast_results.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1225]
2024-10-23 16:08:38,567 root INFO: Blasting orit sequences .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/databases/orit.fas against Trash/tmpxdp6z6og/fixed.input.fasta [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1234]
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:338: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
2024-10-23 16:08:38,797 root INFO: Filtering orit blast results Trash/tmpxdp6z6og/orit_blast_results.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:1239]
2024-10-23 16:08:40,682 root INFO: b'mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory\n' [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/wrappers/init.py:23]
.conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/utils.py:338: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
blast_df.to_csv(blast_results_file, sep='\t', header=True, line_terminator='\n', index=False)
2024-10-23 16:08:41,974 mob_suite.mob_typer INFO: MOB-typer MGE results written to mobtyper_report_test.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:566]
2024-10-23 16:08:41,976 mob_suite.mob_typer INFO: MOB-typer completed and results written
to sample_mobtyper_gene_test.txt [in .conda/envs/mob_suite/lib/python3.11/site-packages/mob_suite/mob_typer.py:614]

I hope you can help me to solve this issue. I installed also gsl=2.5 as indicated here #110 (comment) but the issue persists. I understand I should be predicting some MGE if the test data are positive controls.

Thank you very much.

Pau

[kbessonov1984]

Hello you have some issue with the MASH tool (mash: error while loading shared libraries). Try to install it conda environment manually again. For example conda install "mash==2.3". Try to run mash tool manually on some sketch to see if it works. Also yo can always try to run mob_suite inside a Docker or Singularity container where it is guaranteed to work.

Due to MASH error you are getting empty results unfortunately. But I hope this will be solved easily. You can also install mash via the linux commands apt install mash systemwide