[2024-01-24 12:31:58,398] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,400] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference
[2024-01-24 12:31:59,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,711] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,711] [INFO] Running command: gunzip -c /var/lib/cwl/stge524c0ab-c98a-43bc-9b7b-f8c25b28e29a/GCF_005670695.1_ASM567069v1_genomic.fna.gz | prodigal -d GCF_005670695.1_ASM567069v1_genomic.fna/cds.fna -a GCF_005670695.1_ASM567069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:23,347] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:23,347] [INFO] Task started: HMMsearch
[2024-01-24 12:32:23,347] [INFO] Running command: hmmsearch --tblout GCF_005670695.1_ASM567069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/reference_markers.hmm GCF_005670695.1_ASM567069v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:23,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:23,704] [INFO] Found 6/6 markers.
[2024-01-24 12:32:23,759] [INFO] Query marker FASTA was written to GCF_005670695.1_ASM567069v1_genomic.fna/markers.fasta
[2024-01-24 12:32:23,759] [INFO] Task started: Blastn
[2024-01-24 12:32:23,759] [INFO] Running command: blastn -query GCF_005670695.1_ASM567069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/reference_markers.fasta -out GCF_005670695.1_ASM567069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:24,974] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:24,977] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:24,978] [INFO] Target genome list was writen to GCF_005670695.1_ASM567069v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:24,983] [INFO] Task started: fastANI
[2024-01-24 12:32:24,984] [INFO] Running command: fastANI --query /var/lib/cwl/stge524c0ab-c98a-43bc-9b7b-f8c25b28e29a/GCF_005670695.1_ASM567069v1_genomic.fna.gz --refList GCF_005670695.1_ASM567069v1_genomic.fna/target_genomes.txt --output GCF_005670695.1_ASM567069v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:48,619] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:48,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:48,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:48,635] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:48,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:48,635] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycolicibacterium aubagnense	strain=DSM 45150	GCA_005670695.1	319707	319707	type	True	100.0	2022	2024	95	conclusive
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	88.7349	1514	2024	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	88.6879	1457	2024	95	below_threshold
Mycolicibacterium phocaicum	strain=DSM 45104	GCA_005670655.1	319706	319706	type	True	88.6695	1448	2024	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.3415	925	2024	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.3027	904	2024	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	80.281	859	2024	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.1595	864	2024	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	80.0832	923	2024	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.0525	855	2024	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7747	930	2024	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.4233	778	2024	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	79.4132	787	2024	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.3447	776	2024	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.2942	771	2024	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.0244	669	2024	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.9993	763	2024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:48,637] [INFO] DFAST Taxonomy check result was written to GCF_005670695.1_ASM567069v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:48,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:48,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:48,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/checkm_data
[2024-01-24 12:32:48,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:48,700] [INFO] Task started: CheckM
[2024-01-24 12:32:48,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005670695.1_ASM567069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005670695.1_ASM567069v1_genomic.fna/checkm_input GCF_005670695.1_ASM567069v1_genomic.fna/checkm_result
[2024-01-24 12:33:58,929] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:58,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:58,957] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:58,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:58,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005670695.1_ASM567069v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:58,958] [INFO] Task started: Blastn
[2024-01-24 12:33:58,958] [INFO] Running command: blastn -query GCF_005670695.1_ASM567069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1326557-f015-4ff3-8de7-a1defc11ba2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005670695.1_ASM567069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:00,641] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:00,646] [INFO] Selected 10 target genomes.
[2024-01-24 12:34:00,646] [INFO] Target genome list was writen to GCF_005670695.1_ASM567069v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:00,656] [INFO] Task started: fastANI
[2024-01-24 12:34:00,657] [INFO] Running command: fastANI --query /var/lib/cwl/stge524c0ab-c98a-43bc-9b7b-f8c25b28e29a/GCF_005670695.1_ASM567069v1_genomic.fna.gz --refList GCF_005670695.1_ASM567069v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005670695.1_ASM567069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:14,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:14,824] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:14,824] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_010730955.1	s__Mycobacterium aubagnense	99.9821	2021	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_004363795.1	s__Mycobacterium sp004363795	88.9906	1557	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000878195.1	s__Mycobacterium llatzerense	88.8477	1532	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.29	97.98	0.87	0.81	4	-
GCF_009729075.1	s__Mycobacterium sp009729075	88.7379	1528	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731115.1	s__Mycobacterium phocaicum	88.6864	1456	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.06	95.24	0.87	0.80	8	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	88.5766	1576	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_018326285.1	s__Mycobacterium sp018326285	88.4619	1511	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001905655.1	s__Mycobacterium sp001905655	88.2945	1360	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	79.5764	814	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_018455725.1	s__Mycobacterium sp018455725	79.4393	626	2024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:14,826] [INFO] GTDB search result was written to GCF_005670695.1_ASM567069v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:14,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:14,830] [INFO] DFAST_QC result json was written to GCF_005670695.1_ASM567069v1_genomic.fna/dqc_result.json
[2024-01-24 12:34:14,830] [INFO] DFAST_QC completed!
[2024-01-24 12:34:14,831] [INFO] Total running time: 0h2m16s