[2024-01-24 12:47:05,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference
[2024-01-24 12:47:06,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,934] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg271d7107-f3e5-4df0-b0ca-1c856c388f9f/GCF_010725885.1_ASM1072588v1_genomic.fna.gz | prodigal -d GCF_010725885.1_ASM1072588v1_genomic.fna/cds.fna -a GCF_010725885.1_ASM1072588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:29,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:29,913] [INFO] Task started: HMMsearch
[2024-01-24 12:47:29,913] [INFO] Running command: hmmsearch --tblout GCF_010725885.1_ASM1072588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/reference_markers.hmm GCF_010725885.1_ASM1072588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:30,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:30,212] [INFO] Found 6/6 markers.
[2024-01-24 12:47:30,263] [INFO] Query marker FASTA was written to GCF_010725885.1_ASM1072588v1_genomic.fna/markers.fasta
[2024-01-24 12:47:30,263] [INFO] Task started: Blastn
[2024-01-24 12:47:30,263] [INFO] Running command: blastn -query GCF_010725885.1_ASM1072588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/reference_markers.fasta -out GCF_010725885.1_ASM1072588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,604] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,612] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:31,613] [INFO] Target genome list was writen to GCF_010725885.1_ASM1072588v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:31,622] [INFO] Task started: fastANI
[2024-01-24 12:47:31,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg271d7107-f3e5-4df0-b0ca-1c856c388f9f/GCF_010725885.1_ASM1072588v1_genomic.fna.gz --refList GCF_010725885.1_ASM1072588v1_genomic.fna/target_genomes.txt --output GCF_010725885.1_ASM1072588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:57,473] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:57,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:57,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:57,491] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:57,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:57,491] [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 tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	100.0	2109	2109	95	conclusive
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	99.9939	2106	2109	95	conclusive
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	81.358	1116	2109	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.5036	928	2109	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.3763	945	2109	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.37	941	2109	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.3254	923	2109	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.2903	748	2109	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.1478	924	2109	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.0458	916	2109	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.0441	648	2109	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8401	867	2109	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.6114	895	2109	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5734	847	2109	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.5152	820	2109	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.5037	823	2109	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.4776	769	2109	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.359	769	2109	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.3082	786	2109	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	79.0164	625	2109	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	78.9375	658	2109	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	78.9164	655	2109	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:57,494] [INFO] DFAST Taxonomy check result was written to GCF_010725885.1_ASM1072588v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:57,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:57,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:57,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/checkm_data
[2024-01-24 12:47:57,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:57,554] [INFO] Task started: CheckM
[2024-01-24 12:47:57,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010725885.1_ASM1072588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010725885.1_ASM1072588v1_genomic.fna/checkm_input GCF_010725885.1_ASM1072588v1_genomic.fna/checkm_result
[2024-01-24 12:49:50,930] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:50,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:50,948] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:50,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:50,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010725885.1_ASM1072588v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:50,949] [INFO] Task started: Blastn
[2024-01-24 12:49:50,949] [INFO] Running command: blastn -query GCF_010725885.1_ASM1072588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacea461b-872a-4fd6-8342-b454ec488156/dqc_reference/reference_markers_gtdb.fasta -out GCF_010725885.1_ASM1072588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:52,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:52,990] [INFO] Selected 21 target genomes.
[2024-01-24 12:49:52,990] [INFO] Target genome list was writen to GCF_010725885.1_ASM1072588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:53,019] [INFO] Task started: fastANI
[2024-01-24 12:49:53,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg271d7107-f3e5-4df0-b0ca-1c856c388f9f/GCF_010725885.1_ASM1072588v1_genomic.fna.gz --refList GCF_010725885.1_ASM1072588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010725885.1_ASM1072588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:17,438] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:17,454] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:17,455] [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_010725885.1	s__Mycobacterium tokaiense	100.0	2109	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	conclusive
GCF_001984215.1	s__Mycobacterium sp001984215	84.6544	1503	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015710575.1	s__Mycobacterium sp015710575	81.3511	1113	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	-
GCF_002592005.1	s__Mycobacterium palauense	80.4888	931	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.3495	947	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_001583415.1	s__Mycobacterium phlei	80.3421	928	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_010726955.1	s__Mycobacterium fallax	80.2969	751	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_010731695.1	s__Mycobacterium litorale	80.154	923	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016197405.1	s__Mycobacterium sp016197405	80.0912	926	2109	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	79.997	816	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	79.9807	898	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_001494595.1	s__Mycobacterium sp001494595	79.9324	908	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	79.9082	875	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499995.1	s__Mycobacterium sp001499995	79.8662	861	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	79.7475	882	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_018326285.1	s__Mycobacterium sp018326285	79.7137	782	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002250655.1	s__Mycobacterium sphagni	79.3682	768	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	79.2855	789	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	79.2571	688	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002102155.1	s__Mycobacterium europaeum	79.0355	703	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_002101585.1	s__Mycobacterium engbaekii	79.0319	623	2109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:17,456] [INFO] GTDB search result was written to GCF_010725885.1_ASM1072588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:17,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:17,461] [INFO] DFAST_QC result json was written to GCF_010725885.1_ASM1072588v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:17,461] [INFO] DFAST_QC completed!
[2024-01-24 12:50:17,461] [INFO] Total running time: 0h3m12s