[2024-01-24 14:19:00,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference
[2024-01-24 14:19:02,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,068] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg9731a0ee-f38f-4989-b10d-2618f13c04fa/GCF_002101585.1_ASM210158v1_genomic.fna.gz | prodigal -d GCF_002101585.1_ASM210158v1_genomic.fna/cds.fna -a GCF_002101585.1_ASM210158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:16,465] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:16,466] [INFO] Task started: HMMsearch
[2024-01-24 14:19:16,466] [INFO] Running command: hmmsearch --tblout GCF_002101585.1_ASM210158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/reference_markers.hmm GCF_002101585.1_ASM210158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:16,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:16,751] [INFO] Found 6/6 markers.
[2024-01-24 14:19:16,795] [INFO] Query marker FASTA was written to GCF_002101585.1_ASM210158v1_genomic.fna/markers.fasta
[2024-01-24 14:19:16,796] [INFO] Task started: Blastn
[2024-01-24 14:19:16,796] [INFO] Running command: blastn -query GCF_002101585.1_ASM210158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/reference_markers.fasta -out GCF_002101585.1_ASM210158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:18,037] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:18,041] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:18,041] [INFO] Target genome list was writen to GCF_002101585.1_ASM210158v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:18,046] [INFO] Task started: fastANI
[2024-01-24 14:19:18,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg9731a0ee-f38f-4989-b10d-2618f13c04fa/GCF_002101585.1_ASM210158v1_genomic.fna.gz --refList GCF_002101585.1_ASM210158v1_genomic.fna/target_genomes.txt --output GCF_002101585.1_ASM210158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:32,118] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:32,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:32,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:32,131] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:32,131] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:19:32,131] [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
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	100.0	1459	1463	95	inconclusive
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	95.3331	1322	1463	95	inconclusive
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	95.329	1309	1463	95	inconclusive
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	86.2188	1200	1463	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	85.2949	1129	1463	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	84.6814	1071	1463	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	84.5864	1098	1463	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	84.2976	1049	1463	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	84.2612	1097	1463	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	79.3427	700	1463	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	79.3056	713	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:32,133] [INFO] DFAST Taxonomy check result was written to GCF_002101585.1_ASM210158v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:32,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:32,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:32,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/checkm_data
[2024-01-24 14:19:32,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:32,181] [INFO] Task started: CheckM
[2024-01-24 14:19:32,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101585.1_ASM210158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101585.1_ASM210158v1_genomic.fna/checkm_input GCF_002101585.1_ASM210158v1_genomic.fna/checkm_result
[2024-01-24 14:20:17,507] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:17,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,529] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:17,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:17,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101585.1_ASM210158v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:17,530] [INFO] Task started: Blastn
[2024-01-24 14:20:17,531] [INFO] Running command: blastn -query GCF_002101585.1_ASM210158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cffbf3f-9cda-44c9-8455-2e8fce9a061b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101585.1_ASM210158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:19,252] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:19,255] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:19,255] [INFO] Target genome list was writen to GCF_002101585.1_ASM210158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:19,286] [INFO] Task started: fastANI
[2024-01-24 14:20:19,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg9731a0ee-f38f-4989-b10d-2618f13c04fa/GCF_002101585.1_ASM210158v1_genomic.fna.gz --refList GCF_002101585.1_ASM210158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101585.1_ASM210158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:36,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,193] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:36,194] [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_002101585.1	s__Mycobacterium engbaekii	100.0	1459	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	conclusive
GCF_010729485.1	s__Mycobacterium hiberniae	95.3065	1324	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	86.7441	1194	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673105.1	s__Mycobacterium heraklionense_A	86.396	1178	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	86.2195	1201	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_000455125.1	s__Mycobacterium sp000455125	86.1699	1181	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	85.9941	1088	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102265.1	s__Mycobacterium longobardum	85.2885	1129	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086515.1	s__Mycobacterium arupense	84.7064	1054	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCF_010731755.1	s__Mycobacterium minnesotense	84.5623	1100	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086285.1	s__Mycobacterium kumamotonense	84.2973	1091	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_001667735.1	s__Mycobacterium sp001667735	79.3456	694	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	79.1966	679	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_002863225.1	s__Mycobacterium sp002863225	79.1578	664	1463	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 14:20:36,196] [INFO] GTDB search result was written to GCF_002101585.1_ASM210158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:36,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:36,202] [INFO] DFAST_QC result json was written to GCF_002101585.1_ASM210158v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:36,202] [INFO] DFAST_QC completed!
[2024-01-24 14:20:36,202] [INFO] Total running time: 0h1m35s