[2024-01-24 13:26:11,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:11,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:11,101] [INFO] DQC Reference Directory: /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference
[2024-01-24 13:26:12,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:12,441] [INFO] Task started: Prodigal
[2024-01-24 13:26:12,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c19e779-fa67-4e5a-a723-747fbed20c30/GCF_002101955.1_ASM210195v1_genomic.fna.gz | prodigal -d GCF_002101955.1_ASM210195v1_genomic.fna/cds.fna -a GCF_002101955.1_ASM210195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:26,610] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:26,611] [INFO] Task started: HMMsearch
[2024-01-24 13:26:26,611] [INFO] Running command: hmmsearch --tblout GCF_002101955.1_ASM210195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/reference_markers.hmm GCF_002101955.1_ASM210195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:26,881] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:26,885] [INFO] Found 6/6 markers.
[2024-01-24 13:26:26,938] [INFO] Query marker FASTA was written to GCF_002101955.1_ASM210195v1_genomic.fna/markers.fasta
[2024-01-24 13:26:26,939] [INFO] Task started: Blastn
[2024-01-24 13:26:26,939] [INFO] Running command: blastn -query GCF_002101955.1_ASM210195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/reference_markers.fasta -out GCF_002101955.1_ASM210195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:28,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:28,188] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:28,189] [INFO] Target genome list was writen to GCF_002101955.1_ASM210195v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:28,190] [INFO] Task started: fastANI
[2024-01-24 13:26:28,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c19e779-fa67-4e5a-a723-747fbed20c30/GCF_002101955.1_ASM210195v1_genomic.fna.gz --refList GCF_002101955.1_ASM210195v1_genomic.fna/target_genomes.txt --output GCF_002101955.1_ASM210195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:41,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:41,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:41,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:41,044] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:41,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:41,045] [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 terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	100.0	1478	1484	95	conclusive
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	99.9943	1480	1484	95	conclusive
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	91.2542	1305	1484	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	91.2506	1240	1484	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	87.6476	1186	1484	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	87.5984	1194	1484	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	86.4697	1129	1484	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	84.7101	1102	1484	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	84.4096	1098	1484	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	83.5013	1029	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,047] [INFO] DFAST Taxonomy check result was written to GCF_002101955.1_ASM210195v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:41,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:41,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:41,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/checkm_data
[2024-01-24 13:26:41,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:41,096] [INFO] Task started: CheckM
[2024-01-24 13:26:41,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101955.1_ASM210195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101955.1_ASM210195v1_genomic.fna/checkm_input GCF_002101955.1_ASM210195v1_genomic.fna/checkm_result
[2024-01-24 13:27:24,568] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:24,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:24,650] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:24,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:24,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101955.1_ASM210195v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:24,652] [INFO] Task started: Blastn
[2024-01-24 13:27:24,652] [INFO] Running command: blastn -query GCF_002101955.1_ASM210195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0251d6e-d309-45a5-bbbe-404cdc83d876/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101955.1_ASM210195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:26,463] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:26,468] [INFO] Selected 13 target genomes.
[2024-01-24 13:27:26,469] [INFO] Target genome list was writen to GCF_002101955.1_ASM210195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:26,479] [INFO] Task started: fastANI
[2024-01-24 13:27:26,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c19e779-fa67-4e5a-a723-747fbed20c30/GCF_002101955.1_ASM210195v1_genomic.fna.gz --refList GCF_002101955.1_ASM210195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101955.1_ASM210195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:42,850] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:42,864] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:42,864] [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_010727125.1	s__Mycobacterium terrae	99.9943	1480	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_002086285.1	s__Mycobacterium kumamotonense	91.2542	1305	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_001667945.1	s__Mycobacterium sinense_B	89.175	1206	1484	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	87.7799	1062	1484	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	87.6465	1203	1484	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	87.6417	1186	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102265.1	s__Mycobacterium longobardum	86.4604	1129	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	85.8126	1172	1484	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	85.1611	1165	1484	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	85.0881	1132	1484	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	85.0564	1116	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101585.1	s__Mycobacterium engbaekii	84.3996	1099	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_010731755.1	s__Mycobacterium minnesotense	83.4883	1031	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:42,866] [INFO] GTDB search result was written to GCF_002101955.1_ASM210195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:42,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:42,870] [INFO] DFAST_QC result json was written to GCF_002101955.1_ASM210195v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:42,871] [INFO] DFAST_QC completed!
[2024-01-24 13:27:42,871] [INFO] Total running time: 0h1m32s