[2024-01-24 12:37:37,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,927] [INFO] DQC Reference Directory: /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference
[2024-01-24 12:37:41,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,018] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c45a61f-db92-4ea6-a708-55bac78c77c0/GCF_000975265.2_ASM97526v2_genomic.fna.gz | prodigal -d GCF_000975265.2_ASM97526v2_genomic.fna/cds.fna -a GCF_000975265.2_ASM97526v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:50,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:50,906] [INFO] Task started: HMMsearch
[2024-01-24 12:37:50,906] [INFO] Running command: hmmsearch --tblout GCF_000975265.2_ASM97526v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/reference_markers.hmm GCF_000975265.2_ASM97526v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:51,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:51,110] [INFO] Found 6/6 markers.
[2024-01-24 12:37:51,141] [INFO] Query marker FASTA was written to GCF_000975265.2_ASM97526v2_genomic.fna/markers.fasta
[2024-01-24 12:37:51,141] [INFO] Task started: Blastn
[2024-01-24 12:37:51,141] [INFO] Running command: blastn -query GCF_000975265.2_ASM97526v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/reference_markers.fasta -out GCF_000975265.2_ASM97526v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:51,856] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:51,862] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:51,862] [INFO] Target genome list was writen to GCF_000975265.2_ASM97526v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:51,885] [INFO] Task started: fastANI
[2024-01-24 12:37:51,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c45a61f-db92-4ea6-a708-55bac78c77c0/GCF_000975265.2_ASM97526v2_genomic.fna.gz --refList GCF_000975265.2_ASM97526v2_genomic.fna/target_genomes.txt --output GCF_000975265.2_ASM97526v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:03,625] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:03,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:03,645] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:03,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:03,645] [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
Mycobacterium lepromatosis	strain=FJ924	GCA_000975265.2	480418	480418	type	True	100.0	1088	1090	95	conclusive
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	85.1016	896	1090	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	79.0174	459	1090	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	78.9693	478	1090	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	78.8087	452	1090	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	78.4761	402	1090	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	78.4315	411	1090	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	78.421	401	1090	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	78.3967	400	1090	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	78.3731	392	1090	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	78.3588	406	1090	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	78.1611	400	1090	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	78.1069	411	1090	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	78.0377	359	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,647] [INFO] DFAST Taxonomy check result was written to GCF_000975265.2_ASM97526v2_genomic.fna/tc_result.tsv
[2024-01-24 12:38:03,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:03,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:03,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/checkm_data
[2024-01-24 12:38:03,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:03,683] [INFO] Task started: CheckM
[2024-01-24 12:38:03,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000975265.2_ASM97526v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000975265.2_ASM97526v2_genomic.fna/checkm_input GCF_000975265.2_ASM97526v2_genomic.fna/checkm_result
[2024-01-24 12:38:37,601] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:37,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:37,621] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:37,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:37,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000975265.2_ASM97526v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:37,622] [INFO] Task started: Blastn
[2024-01-24 12:38:37,622] [INFO] Running command: blastn -query GCF_000975265.2_ASM97526v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga8999f53-3233-4131-9d6f-90519d2ac0c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000975265.2_ASM97526v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:38,664] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:38,669] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:38,669] [INFO] Target genome list was writen to GCF_000975265.2_ASM97526v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:38,704] [INFO] Task started: fastANI
[2024-01-24 12:38:38,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c45a61f-db92-4ea6-a708-55bac78c77c0/GCF_000975265.2_ASM97526v2_genomic.fna.gz --refList GCF_000975265.2_ASM97526v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000975265.2_ASM97526v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:51,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:51,657] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:51,658] [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_000966355.1	s__Mycobacterium lepromatosis	99.8811	999	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.85	99.85	0.96	0.96	2	conclusive
GCF_000195855.1	s__Mycobacterium leprae	88.051	965	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.91	1.00	0.99	6	-
GCF_000340435.2	s__Mycobacterium haemophilum	85.0801	898	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_003408705.1	s__Mycobacterium uberis	82.2627	651	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	78.9994	458	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010731535.1	s__Mycobacterium lacus	78.9693	478	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900078675.2	s__Mycobacterium interjectum	78.5525	397	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900232995.1	s__Mycobacterium simulans	78.4761	402	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_002104675.1	s__Mycobacterium decipiens	78.4467	451	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101845.1	s__Mycobacterium riyadhense	78.3873	401	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_002086635.1	s__Mycobacterium alsense	78.3128	373	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCA_003165155.1	s__Mycobacterium sp003165155	78.3077	364	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.39	99.24	0.91	0.88	10	-
GCF_001954195.1	s__Mycobacterium sp001954195	78.3048	428	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_010730195.1	s__Mycobacterium conspicuum	78.1069	411	1090	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:51,662] [INFO] GTDB search result was written to GCF_000975265.2_ASM97526v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:51,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:51,669] [INFO] DFAST_QC result json was written to GCF_000975265.2_ASM97526v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:51,669] [INFO] DFAST_QC completed!
[2024-01-24 12:38:51,669] [INFO] Total running time: 0h1m14s