[2024-01-25 19:41:20,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:20,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:20,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference
[2024-01-25 19:41:21,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:21,938] [INFO] Task started: Prodigal
[2024-01-25 19:41:21,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg95d794ae-b42d-47bf-9cdf-e2a0fb95477c/GCF_025821725.1_ASM2582172v1_genomic.fna.gz | prodigal -d GCF_025821725.1_ASM2582172v1_genomic.fna/cds.fna -a GCF_025821725.1_ASM2582172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:38,933] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:38,934] [INFO] Task started: HMMsearch
[2024-01-25 19:41:38,934] [INFO] Running command: hmmsearch --tblout GCF_025821725.1_ASM2582172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/reference_markers.hmm GCF_025821725.1_ASM2582172v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:39,311] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:39,314] [INFO] Found 6/6 markers.
[2024-01-25 19:41:39,359] [INFO] Query marker FASTA was written to GCF_025821725.1_ASM2582172v1_genomic.fna/markers.fasta
[2024-01-25 19:41:39,360] [INFO] Task started: Blastn
[2024-01-25 19:41:39,360] [INFO] Running command: blastn -query GCF_025821725.1_ASM2582172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/reference_markers.fasta -out GCF_025821725.1_ASM2582172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:40,520] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:40,523] [INFO] Selected 20 target genomes.
[2024-01-25 19:41:40,524] [INFO] Target genome list was writen to GCF_025821725.1_ASM2582172v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:40,528] [INFO] Task started: fastANI
[2024-01-25 19:41:40,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d794ae-b42d-47bf-9cdf-e2a0fb95477c/GCF_025821725.1_ASM2582172v1_genomic.fna.gz --refList GCF_025821725.1_ASM2582172v1_genomic.fna/target_genomes.txt --output GCF_025821725.1_ASM2582172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:04,628] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:04,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:04,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:04,641] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:42:04,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:04,641] [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 chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	99.9919	1701	1702	95	conclusive
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	99.9878	1700	1702	95	conclusive
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	82.0137	1086	1702	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	81.9065	830	1702	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	81.8928	838	1702	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	81.3383	937	1702	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	80.9822	718	1702	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.9628	877	1702	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	80.9602	709	1702	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	80.4862	901	1702	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.3093	886	1702	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.2568	829	1702	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	80.1607	834	1702	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.1251	751	1702	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.087	850	1702	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	80.0811	826	1702	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.043	838	1702	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	80.0373	803	1702	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0195	876	1702	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.9773	880	1702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:04,642] [INFO] DFAST Taxonomy check result was written to GCF_025821725.1_ASM2582172v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:04,643] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:04,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:04,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/checkm_data
[2024-01-25 19:42:04,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:04,695] [INFO] Task started: CheckM
[2024-01-25 19:42:04,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821725.1_ASM2582172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821725.1_ASM2582172v1_genomic.fna/checkm_input GCF_025821725.1_ASM2582172v1_genomic.fna/checkm_result
[2024-01-25 19:42:59,519] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:59,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:59,538] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:59,538] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:59,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821725.1_ASM2582172v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:59,539] [INFO] Task started: Blastn
[2024-01-25 19:42:59,539] [INFO] Running command: blastn -query GCF_025821725.1_ASM2582172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bad802b-bccc-46a7-9fbc-684c70cc1a79/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821725.1_ASM2582172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:01,279] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:01,281] [INFO] Selected 23 target genomes.
[2024-01-25 19:43:01,282] [INFO] Target genome list was writen to GCF_025821725.1_ASM2582172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:01,287] [INFO] Task started: fastANI
[2024-01-25 19:43:01,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d794ae-b42d-47bf-9cdf-e2a0fb95477c/GCF_025821725.1_ASM2582172v1_genomic.fna.gz --refList GCF_025821725.1_ASM2582172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821725.1_ASM2582172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:29,991] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:30,005] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:30,005] [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_900637205.1	s__Mycobacterium chitae	99.9919	1701	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_010729895.1	s__Mycobacterium confluentis	81.9935	1089	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667265.1	s__Mycobacterium sp001667265	81.9334	1058	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726955.1	s__Mycobacterium fallax	81.8564	843	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_002592005.1	s__Mycobacterium palauense	81.3441	936	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.2637	952	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_004014795.1	s__Mycobacterium brumae	80.9443	712	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCF_900108565.1	s__Mycobacterium rutilum	80.9182	883	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	80.822	948	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.7896	823	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187505.1	s__Mycobacterium goodii_B	80.6265	911	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	80.6241	927	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668625.1	s__Mycobacterium sp001668625	80.5817	690	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.4987	914	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.461	937	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	80.3892	845	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_010725725.1	s__Mycobacterium pulveris	80.3299	883	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014805.1	s__Mycobacterium elephantis	80.2841	876	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_002838065.1	s__Mycobacterium sp002838065	80.2494	818	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	80.1883	828	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	80.1745	862	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	80.0456	819	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_010727475.1	s__Mycobacterium mageritense	79.9882	878	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:30,007] [INFO] GTDB search result was written to GCF_025821725.1_ASM2582172v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:30,008] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:30,011] [INFO] DFAST_QC result json was written to GCF_025821725.1_ASM2582172v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:30,011] [INFO] DFAST_QC completed!
[2024-01-25 19:43:30,012] [INFO] Total running time: 0h2m9s