[2024-01-25 18:12:50,846] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:50,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:50,848] [INFO] DQC Reference Directory: /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference
[2024-01-25 18:12:52,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:52,007] [INFO] Task started: Prodigal
[2024-01-25 18:12:52,007] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4c7419c-5180-4cdb-bbd1-ce10cf070997/GCF_025821845.1_ASM2582184v1_genomic.fna.gz | prodigal -d GCF_025821845.1_ASM2582184v1_genomic.fna/cds.fna -a GCF_025821845.1_ASM2582184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:10,957] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:10,957] [INFO] Task started: HMMsearch
[2024-01-25 18:13:10,957] [INFO] Running command: hmmsearch --tblout GCF_025821845.1_ASM2582184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/reference_markers.hmm GCF_025821845.1_ASM2582184v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:11,216] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:11,217] [INFO] Found 6/6 markers.
[2024-01-25 18:13:11,270] [INFO] Query marker FASTA was written to GCF_025821845.1_ASM2582184v1_genomic.fna/markers.fasta
[2024-01-25 18:13:11,270] [INFO] Task started: Blastn
[2024-01-25 18:13:11,271] [INFO] Running command: blastn -query GCF_025821845.1_ASM2582184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/reference_markers.fasta -out GCF_025821845.1_ASM2582184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:12,328] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:12,331] [INFO] Selected 11 target genomes.
[2024-01-25 18:13:12,331] [INFO] Target genome list was writen to GCF_025821845.1_ASM2582184v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:12,334] [INFO] Task started: fastANI
[2024-01-25 18:13:12,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c7419c-5180-4cdb-bbd1-ce10cf070997/GCF_025821845.1_ASM2582184v1_genomic.fna.gz --refList GCF_025821845.1_ASM2582184v1_genomic.fna/target_genomes.txt --output GCF_025821845.1_ASM2582184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:28,060] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:28,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:28,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:28,069] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:28,069] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:28,069] [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
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	99.9489	2061	2138	95	conclusive
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	90.0036	1540	2138	95	below_threshold
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	89.3868	1490	2138	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	89.3348	1551	2138	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	84.4091	1426	2138	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	84.4043	1444	2138	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	84.3926	1348	2138	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.3562	1281	2138	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	84.1156	1321	2138	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.1267	1246	2138	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.4714	1273	2138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:28,071] [INFO] DFAST Taxonomy check result was written to GCF_025821845.1_ASM2582184v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:28,072] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:28,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:28,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/checkm_data
[2024-01-25 18:13:28,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:28,135] [INFO] Task started: CheckM
[2024-01-25 18:13:28,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821845.1_ASM2582184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821845.1_ASM2582184v1_genomic.fna/checkm_input GCF_025821845.1_ASM2582184v1_genomic.fna/checkm_result
[2024-01-25 18:14:24,537] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:24,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:24,562] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:24,562] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:24,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821845.1_ASM2582184v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:24,563] [INFO] Task started: Blastn
[2024-01-25 18:14:24,563] [INFO] Running command: blastn -query GCF_025821845.1_ASM2582184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1e57ec1-1413-45b5-90d6-d327c28fcd28/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821845.1_ASM2582184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:26,104] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:26,107] [INFO] Selected 15 target genomes.
[2024-01-25 18:14:26,107] [INFO] Target genome list was writen to GCF_025821845.1_ASM2582184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:26,112] [INFO] Task started: fastANI
[2024-01-25 18:14:26,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c7419c-5180-4cdb-bbd1-ce10cf070997/GCF_025821845.1_ASM2582184v1_genomic.fna.gz --refList GCF_025821845.1_ASM2582184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821845.1_ASM2582184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:47,573] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:47,583] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:47,583] [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_002102255.1	s__Mycobacterium nebraskense	99.9489	2061	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	conclusive
GCF_001665605.1	s__Mycobacterium sp001665605	90.3526	1472	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_010731595.1	s__Mycobacterium seoulense	90.0108	1539	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667585.1	s__Mycobacterium sp001667585	89.9519	1442	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	89.94	1644	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667075.1	s__Mycobacterium sp001667075	89.7706	1467	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_001666835.1	s__Mycobacterium sp001666835	89.5177	1413	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_010731655.1	s__Mycobacterium paraseoulense	89.3757	1547	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240975.1	s__Mycobacterium sp900240975	88.8219	1456	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001907675.1	s__Mycobacterium paraffinicum	88.7338	1501	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	88.6613	1481	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001667735.1	s__Mycobacterium sp001667735	88.6088	1406	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_010731775.1	s__Mycobacterium mantenii	84.4076	1444	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCA_004298145.1	s__Mycobacterium sp004298145	84.2342	1338	2138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	82.4797	1272	2138	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 18:14:47,584] [INFO] GTDB search result was written to GCF_025821845.1_ASM2582184v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:47,585] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:47,588] [INFO] DFAST_QC result json was written to GCF_025821845.1_ASM2582184v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:47,588] [INFO] DFAST_QC completed!
[2024-01-25 18:14:47,588] [INFO] Total running time: 0h1m57s