[2024-01-24 10:47:40,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg8432622c-de20-429e-9aa5-068c63fcba9f/GCF_010093495.1_ASM1009349v1_genomic.fna.gz | prodigal -d GCF_010093495.1_ASM1009349v1_genomic.fna/cds.fna -a GCF_010093495.1_ASM1009349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:58,848] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:58,849] [INFO] Task started: HMMsearch
[2024-01-24 10:47:58,849] [INFO] Running command: hmmsearch --tblout GCF_010093495.1_ASM1009349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/reference_markers.hmm GCF_010093495.1_ASM1009349v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:59,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:59,142] [INFO] Found 6/6 markers.
[2024-01-24 10:47:59,184] [INFO] Query marker FASTA was written to GCF_010093495.1_ASM1009349v1_genomic.fna/markers.fasta
[2024-01-24 10:47:59,184] [INFO] Task started: Blastn
[2024-01-24 10:47:59,184] [INFO] Running command: blastn -query GCF_010093495.1_ASM1009349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/reference_markers.fasta -out GCF_010093495.1_ASM1009349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:00,291] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:00,295] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:00,295] [INFO] Target genome list was writen to GCF_010093495.1_ASM1009349v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:00,300] [INFO] Task started: fastANI
[2024-01-24 10:48:00,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg8432622c-de20-429e-9aa5-068c63fcba9f/GCF_010093495.1_ASM1009349v1_genomic.fna.gz --refList GCF_010093495.1_ASM1009349v1_genomic.fna/target_genomes.txt --output GCF_010093495.1_ASM1009349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:11,444] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:11,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:11,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:11,463] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:11,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:11,463] [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 kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	100.0	1499	1510	95	conclusive
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	98.5274	1309	1510	95	conclusive
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	91.089	1276	1510	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	91.0638	1262	1510	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	87.3283	1177	1510	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	87.3248	1163	1510	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	84.7741	1063	1510	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	84.2296	1064	1510	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	80.1795	792	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:11,466] [INFO] DFAST Taxonomy check result was written to GCF_010093495.1_ASM1009349v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:11,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:11,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:11,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/checkm_data
[2024-01-24 10:48:11,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:11,522] [INFO] Task started: CheckM
[2024-01-24 10:48:11,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093495.1_ASM1009349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093495.1_ASM1009349v1_genomic.fna/checkm_input GCF_010093495.1_ASM1009349v1_genomic.fna/checkm_result
[2024-01-24 10:48:54,530] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:54,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:54,556] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:54,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:54,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093495.1_ASM1009349v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:54,557] [INFO] Task started: Blastn
[2024-01-24 10:48:54,557] [INFO] Running command: blastn -query GCF_010093495.1_ASM1009349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93c8625a-347c-4912-84f0-7748c8849301/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093495.1_ASM1009349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:56,189] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:56,192] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:56,192] [INFO] Target genome list was writen to GCF_010093495.1_ASM1009349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:56,200] [INFO] Task started: fastANI
[2024-01-24 10:48:56,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg8432622c-de20-429e-9aa5-068c63fcba9f/GCF_010093495.1_ASM1009349v1_genomic.fna.gz --refList GCF_010093495.1_ASM1009349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093495.1_ASM1009349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:11,986] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:12,010] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:12,010] [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_002086285.1	s__Mycobacterium kumamotonense	98.5274	1309	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	conclusive
GCF_010727125.1	s__Mycobacterium terrae	91.0836	1276	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001667375.1	s__Mycobacterium sinense_A	89.0422	1163	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_001667945.1	s__Mycobacterium sinense_B	88.9141	1171	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_003284925.1	s__Mycobacterium algericum_A	88.2105	1122	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086455.1	s__Mycobacterium algericum	87.3419	1173	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_002101885.1	s__Mycobacterium senuense	87.3355	1162	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	85.5537	1124	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	85.0245	1058	1510	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	85.0196	1131	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_000455125.1	s__Mycobacterium sp000455125	84.978	1092	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	84.7791	1062	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_002101585.1	s__Mycobacterium engbaekii	84.2402	1064	1510	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 10:49:12,012] [INFO] GTDB search result was written to GCF_010093495.1_ASM1009349v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:12,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:12,016] [INFO] DFAST_QC result json was written to GCF_010093495.1_ASM1009349v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:12,016] [INFO] DFAST_QC completed!
[2024-01-24 10:49:12,016] [INFO] Total running time: 0h1m31s