[2024-01-24 11:26:38,808] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference
[2024-01-24 11:26:40,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,118] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bf403c0-44c2-404a-885c-c84e8340b0e8/GCF_025821605.1_ASM2582160v1_genomic.fna.gz | prodigal -d GCF_025821605.1_ASM2582160v1_genomic.fna/cds.fna -a GCF_025821605.1_ASM2582160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:53,941] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:53,942] [INFO] Task started: HMMsearch
[2024-01-24 11:26:53,942] [INFO] Running command: hmmsearch --tblout GCF_025821605.1_ASM2582160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/reference_markers.hmm GCF_025821605.1_ASM2582160v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:54,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:54,215] [INFO] Found 6/6 markers.
[2024-01-24 11:26:54,259] [INFO] Query marker FASTA was written to GCF_025821605.1_ASM2582160v1_genomic.fna/markers.fasta
[2024-01-24 11:26:54,259] [INFO] Task started: Blastn
[2024-01-24 11:26:54,259] [INFO] Running command: blastn -query GCF_025821605.1_ASM2582160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/reference_markers.fasta -out GCF_025821605.1_ASM2582160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:55,453] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:55,456] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:55,457] [INFO] Target genome list was writen to GCF_025821605.1_ASM2582160v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:55,461] [INFO] Task started: fastANI
[2024-01-24 11:26:55,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf403c0-44c2-404a-885c-c84e8340b0e8/GCF_025821605.1_ASM2582160v1_genomic.fna.gz --refList GCF_025821605.1_ASM2582160v1_genomic.fna/target_genomes.txt --output GCF_025821605.1_ASM2582160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:07,322] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:07,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:07,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:07,336] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:27:07,336] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:07,336] [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 hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	99.9919	1439	1440	95	inconclusive
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	99.979	1412	1440	95	inconclusive
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	95.4153	1299	1440	95	inconclusive
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	86.0405	1219	1440	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	85.2229	1125	1440	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	84.7521	1066	1440	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	84.6273	1069	1440	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	84.6216	1085	1440	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	84.1728	1056	1440	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	84.1559	1082	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:07,338] [INFO] DFAST Taxonomy check result was written to GCF_025821605.1_ASM2582160v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:07,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:07,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:07,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/checkm_data
[2024-01-24 11:27:07,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:07,386] [INFO] Task started: CheckM
[2024-01-24 11:27:07,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821605.1_ASM2582160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821605.1_ASM2582160v1_genomic.fna/checkm_input GCF_025821605.1_ASM2582160v1_genomic.fna/checkm_result
[2024-01-24 11:27:51,939] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:51,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,964] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:51,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:51,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821605.1_ASM2582160v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:51,965] [INFO] Task started: Blastn
[2024-01-24 11:27:51,966] [INFO] Running command: blastn -query GCF_025821605.1_ASM2582160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg504a23b9-a9bd-4e26-afcc-7f4ed1d3977f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821605.1_ASM2582160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:53,685] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:53,689] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:53,690] [INFO] Target genome list was writen to GCF_025821605.1_ASM2582160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:53,698] [INFO] Task started: fastANI
[2024-01-24 11:27:53,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bf403c0-44c2-404a-885c-c84e8340b0e8/GCF_025821605.1_ASM2582160v1_genomic.fna.gz --refList GCF_025821605.1_ASM2582160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821605.1_ASM2582160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:07,228] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:07,248] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:28:07,249] [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_010729485.1	s__Mycobacterium hiberniae	99.9919	1439	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	inconclusive
GCF_002101585.1	s__Mycobacterium engbaekii	95.4153	1299	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	inconclusive
GCF_001021505.1	s__Mycobacterium heraklionense_B	86.6946	1198	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	86.2365	1159	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_001673105.1	s__Mycobacterium heraklionense_A	86.2158	1193	1440	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	86.0402	1217	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	85.9553	1093	1440	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	85.2084	1126	1440	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	84.753	1066	1440	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	84.6056	1087	1440	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	84.1356	1084	1440	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,251] [INFO] GTDB search result was written to GCF_025821605.1_ASM2582160v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:07,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:07,255] [INFO] DFAST_QC result json was written to GCF_025821605.1_ASM2582160v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:07,255] [INFO] DFAST_QC completed!
[2024-01-24 11:28:07,255] [INFO] Total running time: 0h1m28s