Error during gtdbtk classify_wf : No such gtdbtk.bac120.summary.tsv

GTDB-Tk
1

Hi,

Please help me to resolve this error:

[2023-01-11 16:14:07] INFO: GTDB-Tk v2.1.0
[2023-01-11 16:14:07] INFO: gtdbtk classify_wf --extension fa --cpus 10 --genome_dir /home/IAME/microcovid/results/AJ05S_210121/Binning/ --out_dir /home/IAME/microcovid/results/AJ05S_210121/gtdbtk
[2023-01-11 16:14:07] INFO: Using GTDB-Tk reference data version r207: /home/IAME/db/gtdbtk-2.1.0/release207_v2
[2023-01-11 16:14:07] INFO: Identifying markers in 5 genomes with 10 threads.
[2023-01-11 16:14:07] TASK: Running Prodigal V2.6.3 to identify genes.
[2023-01-11 16:14:09] INFO: Completed 5 genomes in 1.65 seconds (3.04 genomes/second).
[2023-01-11 16:14:09] WARNING: Prodigal skipped 5 genomes due to pre-existing data, see warnings.log
[2023-01-11 16:14:09] TASK: Identifying TIGRFAM protein families.
[2023-01-11 16:14:09] INFO: Completed 5 genomes in 0.18 seconds (27.85 genomes/second).
[2023-01-11 16:14:09] WARNING: TIGRFAM skipped 5 genomes due to pre-existing data, see warnings.log
[2023-01-11 16:14:09] TASK: Identifying Pfam protein families.
[2023-01-11 16:14:09] INFO: Completed 5 genomes in 0.18 seconds (28.29 genomes/second).
[2023-01-11 16:14:09] WARNING: Pfam skipped 5 genomes due to pre-existing data, see warnings.log
[2023-01-11 16:14:09] INFO: Annotations done using HMMER 3.1b2 (February 2015).
[2023-01-11 16:14:09] TASK: Summarising identified marker genes.
[2023-01-11 16:14:11] INFO: Completed 5 genomes in 1.51 seconds (3.30 genomes/second).
[2023-01-11 16:14:11] INFO: Done.
[2023-01-11 16:14:13] INFO: Aligning markers in 5 genomes with 10 CPUs.
[2023-01-11 16:14:13] INFO: Processing 5 genomes identified as bacterial.
[2023-01-11 16:15:35] INFO: Read concatenated alignment for 62,291 GTDB genomes.
[2023-01-11 16:15:35] TASK: Generating concatenated alignment for each marker.
[2023-01-11 16:15:36] INFO: Completed 5 genomes in 0.66 seconds (7.61 genomes/second).
[2023-01-11 16:15:37] TASK: Aligning 1 identified markers using hmmalign 3.1b2 (February 2015).
[2023-01-11 16:15:38] INFO: Completed 1 marker in 0.29 seconds (3.45 markers/second).
[2023-01-11 16:15:38] WARNING: Filtered 4 genomes with no bacterial or archaeal marker.
[2023-01-11 16:15:38] TASK: Masking columns of bacterial multiple sequence alignment using canonical mask.
[2023-01-11 16:18:19] INFO: Completed 62,292 sequences in 2.68 minutes (23,205.37 sequences/minute).
[2023-01-11 16:18:19] INFO: Masked bacterial alignment from 41,084 to 5,036 AAs.
[2023-01-11 16:18:19] INFO: 1 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA.
[2023-01-11 16:18:19] INFO: Creating concatenated alignment for 62,291 bacterial GTDB and user genomes.
[2023-01-11 16:18:42] INFO: All bacterial user genomes have been filtered out.
[2023-01-11 16:18:42] INFO: Done.
[2023-01-11 16:18:44] ERROR: Uncontrolled exit resulting from an unexpected error.

================================================================================
EXCEPTION: FileNotFoundError
  MESSAGE: [Errno 2] No such file or directory: '/home/IAME/microcovid/results/AJ05S_210121/gtdbtk/classify/gtdbtk.bac120.summary.tsv'
________________________________________________________________________________

Traceback (most recent call last):
  File "/usr/bin/miniconda2/envs/gtdbtk-2.1.0/lib/python3.8/site-packages/gtdbtk/__main__.py", line 98, in main
    gt_parser.parse_options(args)
  File "/usr/bin/miniconda2/envs/gtdbtk-2.1.0/lib/python3.8/site-packages/gtdbtk/main.py", line 834, in parse_options
    self.classify(options)
  File "/usr/bin/miniconda2/envs/gtdbtk-2.1.0/lib/python3.8/site-packages/gtdbtk/main.py", line 458, in classify
    classify.run(genomes=genomes,
  File "/usr/bin/miniconda2/envs/gtdbtk-2.1.0/lib/python3.8/site-packages/gtdbtk/classify.py", line 372, in run
    summary_file.write()
  File "/usr/bin/miniconda2/envs/gtdbtk-2.1.0/lib/python3.8/site-packages/gtdbtk/io/classify_summary.py", line 107, in write
    with open(self.path, 'w') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/home/IAME/microcovid/results/AJ05S_210121/gtdbtk/classify/gtdbtk.bac120.summary.tsv'
================================================================================
2

Hi,

It appears all your input genomes are being filtered since they either lack any of the expected bacterial or archaeal marker genomes (4 genomes) or have exceedingly few marker genes (1 genome). In general, this is unusual so I suspect your input data is not bacterial or archaeal genome assemblies, or that these assemblies are of poor quality. Have you assessed the quality of your genomes with a tool like CheckM or BUSCO?

Cheers,
Donovan