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"AttributeError: 'Namespace' object has no attribute 'scratch_dir' " was returned when running with option classify_wf #297

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6x16 opened this issue Dec 11, 2020 · 0 comments · Fixed by #306
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error Help required for a GTDB-Tk error.

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@6x16
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6x16 commented Dec 11, 2020

I have installed GTDB-Tk 1.3.0 by conda today and tried to analyse some of my FNA files. However, the program crashed and returned an error at the end:

AttributeError: 'Namespace' object has no attribute 'scratch_dir'

Could anyone help me to solve it?

I have attached my command and the whole output result below.

gtdbtk classify_wf --genome_dir trial_input/ --out_dir trial_output --cpus 8

[2020-12-12 00:57:46] INFO: GTDB-Tk v1.3.0
[2020-12-12 00:57:46] INFO: gtdbtk classify_wf --genome_dir trial_input/ --out_dir trial_output --cpus 8
[2020-12-12 00:57:46] INFO: Using GTDB-Tk reference data version r95: /disk/anaconda3/envs/Gtdbtk/share/gtdbtk-1.3.0/db/
[2020-12-12 00:57:47] INFO: Identifying markers in 16 genomes with 8 threads.
[2020-12-12 00:57:47] INFO: Running Prodigal V2.6.3 to identify genes.
==> Processed 16/16 (100%) genomes [ 3.74s/it, ETA 00:00]
[2020-12-12 00:58:47] INFO: Identifying TIGRFAM protein families.
==> Processed 16/16 (100%) genomes [ 1.44s/it, ETA 00:00]
[2020-12-12 00:59:11] INFO: Identifying Pfam protein families.
==> Processed 16/16 (100%) genomes [ 3.05it/s, ETA 00:00]
[2020-12-12 00:59:16] INFO: Annotations done using HMMER 3.1b2 (February 2015).
[2020-12-12 00:59:17] INFO: Done.
[2020-12-12 00:59:18] INFO: Aligning markers in 16 genomes with 8 threads.
[2020-12-12 00:59:18] INFO: Processing 15 genomes identified as bacterial.
[2020-12-12 00:59:21] INFO: Read concatenated alignment for 30,238 GTDB genomes.
==> Aligned 15/15 (100%) genomes [ 2.94s/it, ETA 00:00]
[2020-12-12 01:00:06] INFO: Masking columns of bacterial multiple sequence alignment using canonical mask.
==> Masked 30253/30253 (100%) alignments [690.06it/s, ETA 00:00]
[2020-12-12 01:00:50] INFO: Masked bacterial alignment from 41,155 to 5,040 AAs.
[2020-12-12 01:00:50] INFO: Creating concatenated alignment for 30,253 bacterial GTDB and user genomes.
[2020-12-12 01:01:18] INFO: Creating concatenated alignment for 15 bacterial user genomes.
[2020-12-12 01:01:19] INFO: Processing 1 genomes identified as archaeal.
[2020-12-12 01:01:19] INFO: Read concatenated alignment for 1,672 GTDB genomes.
==> Aligned 1/1 (100%) genomes [ 9.25s/it, ETA 00:00]
[2020-12-12 01:01:28] INFO: Masking columns of archaeal multiple sequence alignment using canonical mask.
==> Masked 1673/1673 (100%) alignments [816.53it/s, ETA 00:00]
[2020-12-12 01:01:31] INFO: Masked archaeal alignment from 32,675 to 5,124 AAs.
[2020-12-12 01:01:31] INFO: Creating concatenated alignment for 1,673 archaeal GTDB and user genomes.
[2020-12-12 01:01:31] INFO: Creating concatenated alignment for 1 archaeal user genomes.
[2020-12-12 01:01:31] INFO: Done.
Unexpected error: <class 'AttributeError'>
Traceback (most recent call last):
File "/disk/anaconda3/bin/gtdbtk", line 389, in
gt_parser.parse_options(args)
File "/disk/anaconda3/envs/Gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 754, in parse_options
self.classify(options)
File "/disk/anaconda3/envs/Gtdbtk/lib/python3.8/site-packages/gtdbtk/main.py", line 475, in classify
if options.scratch_dir:
AttributeError: 'Namespace' object has no attribute 'scratch_dir'

@6x16 6x16 added the error Help required for a GTDB-Tk error. label Dec 11, 2020
@aaronmussig aaronmussig linked a pull request Feb 2, 2021 that will close this issue
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