[2024-01-25 19:03:05,664] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:05,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:05,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference
[2024-01-25 19:03:06,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:06,845] [INFO] Task started: Prodigal
[2024-01-25 19:03:06,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg127e55c3-049e-4c40-bd1a-625df63eb686/GCF_025821425.1_ASM2582142v1_genomic.fna.gz | prodigal -d GCF_025821425.1_ASM2582142v1_genomic.fna/cds.fna -a GCF_025821425.1_ASM2582142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:19,080] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:19,080] [INFO] Task started: HMMsearch
[2024-01-25 19:03:19,080] [INFO] Running command: hmmsearch --tblout GCF_025821425.1_ASM2582142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/reference_markers.hmm GCF_025821425.1_ASM2582142v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:19,375] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:19,376] [INFO] Found 6/6 markers.
[2024-01-25 19:03:19,415] [INFO] Query marker FASTA was written to GCF_025821425.1_ASM2582142v1_genomic.fna/markers.fasta
[2024-01-25 19:03:19,415] [INFO] Task started: Blastn
[2024-01-25 19:03:19,415] [INFO] Running command: blastn -query GCF_025821425.1_ASM2582142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/reference_markers.fasta -out GCF_025821425.1_ASM2582142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:20,567] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:20,571] [INFO] Selected 16 target genomes.
[2024-01-25 19:03:20,571] [INFO] Target genome list was writen to GCF_025821425.1_ASM2582142v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:20,583] [INFO] Task started: fastANI
[2024-01-25 19:03:20,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg127e55c3-049e-4c40-bd1a-625df63eb686/GCF_025821425.1_ASM2582142v1_genomic.fna.gz --refList GCF_025821425.1_ASM2582142v1_genomic.fna/target_genomes.txt --output GCF_025821425.1_ASM2582142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:38,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:38,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:38,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:38,302] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:03:38,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:38,302] [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 minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	99.9945	1379	1380	95	conclusive
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	99.9818	1355	1380	95	conclusive
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	90.7455	1202	1380	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	85.3163	1094	1380	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	84.7381	1080	1380	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	84.7131	1051	1380	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	84.5485	1075	1380	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	84.4926	1105	1380	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	83.2547	1017	1380	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	78.9056	590	1380	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	78.5373	530	1380	95	below_threshold
Mycolicibacterium agri	strain=CCUG37673	GCA_002553505.1	36811	36811	type	True	78.5184	519	1380	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	78.2497	455	1380	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	78.2421	517	1380	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	78.154	515	1380	95	below_threshold
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	78.086	487	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:38,312] [INFO] DFAST Taxonomy check result was written to GCF_025821425.1_ASM2582142v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:38,313] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:38,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:38,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/checkm_data
[2024-01-25 19:03:38,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:38,365] [INFO] Task started: CheckM
[2024-01-25 19:03:38,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821425.1_ASM2582142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821425.1_ASM2582142v1_genomic.fna/checkm_input GCF_025821425.1_ASM2582142v1_genomic.fna/checkm_result
[2024-01-25 19:04:16,953] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:16,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:16,973] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:16,973] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:16,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821425.1_ASM2582142v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:16,976] [INFO] Task started: Blastn
[2024-01-25 19:04:16,976] [INFO] Running command: blastn -query GCF_025821425.1_ASM2582142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7fcf54-471e-421f-928a-6d40a117ea9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821425.1_ASM2582142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:18,766] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:18,769] [INFO] Selected 18 target genomes.
[2024-01-25 19:04:18,769] [INFO] Target genome list was writen to GCF_025821425.1_ASM2582142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:18,781] [INFO] Task started: fastANI
[2024-01-25 19:04:18,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg127e55c3-049e-4c40-bd1a-625df63eb686/GCF_025821425.1_ASM2582142v1_genomic.fna.gz --refList GCF_025821425.1_ASM2582142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821425.1_ASM2582142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:39,125] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:39,136] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:39,136] [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_010731755.1	s__Mycobacterium minnesotense	99.9945	1379	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002086515.1	s__Mycobacterium arupense	90.7303	1204	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	86.4584	1148	1380	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	86.0041	1169	1380	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	85.9781	1117	1380	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	85.8331	1124	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	85.2948	1096	1380	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	84.7424	1079	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_002102265.1	s__Mycobacterium longobardum	84.7274	1049	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729485.1	s__Mycobacterium hiberniae	84.5247	1103	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_010726645.1	s__Mycobacterium duvalii	78.713	569	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002553505.1	s__Mycobacterium agri	78.5364	516	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001668615.1	s__Mycobacterium sp001668615	78.4073	494	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	78.2716	513	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010728925.1	s__Mycobacterium gadium	78.2661	452	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726765.1	s__Mycobacterium gallinarum	78.2192	466	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086795.1	s__Mycobacterium tusciae	78.1056	484	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591975.1	s__Mycobacterium neglectum	77.9813	471	1380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:39,138] [INFO] GTDB search result was written to GCF_025821425.1_ASM2582142v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:39,139] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:39,142] [INFO] DFAST_QC result json was written to GCF_025821425.1_ASM2582142v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:39,142] [INFO] DFAST_QC completed!
[2024-01-25 19:04:39,142] [INFO] Total running time: 0h1m33s