[2024-01-24 14:13:18,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference
[2024-01-24 14:13:20,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:20,089] [INFO] Task started: Prodigal
[2024-01-24 14:13:20,090] [INFO] Running command: gunzip -c /var/lib/cwl/stga3003a1f-9461-4652-b69e-c190f0c140fe/GCF_010731775.1_ASM1073177v1_genomic.fna.gz | prodigal -d GCF_010731775.1_ASM1073177v1_genomic.fna/cds.fna -a GCF_010731775.1_ASM1073177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:44,382] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:44,383] [INFO] Task started: HMMsearch
[2024-01-24 14:13:44,383] [INFO] Running command: hmmsearch --tblout GCF_010731775.1_ASM1073177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/reference_markers.hmm GCF_010731775.1_ASM1073177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:44,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:44,730] [INFO] Found 6/6 markers.
[2024-01-24 14:13:44,780] [INFO] Query marker FASTA was written to GCF_010731775.1_ASM1073177v1_genomic.fna/markers.fasta
[2024-01-24 14:13:44,781] [INFO] Task started: Blastn
[2024-01-24 14:13:44,781] [INFO] Running command: blastn -query GCF_010731775.1_ASM1073177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/reference_markers.fasta -out GCF_010731775.1_ASM1073177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:45,982] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:45,986] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:45,987] [INFO] Target genome list was writen to GCF_010731775.1_ASM1073177v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:45,998] [INFO] Task started: fastANI
[2024-01-24 14:13:45,999] [INFO] Running command: fastANI --query /var/lib/cwl/stga3003a1f-9461-4652-b69e-c190f0c140fe/GCF_010731775.1_ASM1073177v1_genomic.fna.gz --refList GCF_010731775.1_ASM1073177v1_genomic.fna/target_genomes.txt --output GCF_010731775.1_ASM1073177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:01,276] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:01,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:01,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:01,294] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:01,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:01,294] [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 mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	100.0	2061	2061	95	conclusive
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	99.9635	1974	2061	95	conclusive
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	89.4568	1557	2061	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	89.4467	1562	2061	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	88.2652	1412	2061	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	86.9734	1495	2061	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	86.9593	1496	2061	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	86.8778	1527	2061	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	86.7286	1489	2061	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	86.7274	1453	2061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:01,297] [INFO] DFAST Taxonomy check result was written to GCF_010731775.1_ASM1073177v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:01,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:01,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:01,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/checkm_data
[2024-01-24 14:14:01,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:01,356] [INFO] Task started: CheckM
[2024-01-24 14:14:01,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731775.1_ASM1073177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731775.1_ASM1073177v1_genomic.fna/checkm_input GCF_010731775.1_ASM1073177v1_genomic.fna/checkm_result
[2024-01-24 14:15:07,139] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:07,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:07,164] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:07,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:07,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731775.1_ASM1073177v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:07,165] [INFO] Task started: Blastn
[2024-01-24 14:15:07,165] [INFO] Running command: blastn -query GCF_010731775.1_ASM1073177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e6a7ab7-2f4d-4c2d-a3ec-61b3f3bc79cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731775.1_ASM1073177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:08,826] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:08,830] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:08,831] [INFO] Target genome list was writen to GCF_010731775.1_ASM1073177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:08,849] [INFO] Task started: fastANI
[2024-01-24 14:15:08,849] [INFO] Running command: fastANI --query /var/lib/cwl/stga3003a1f-9461-4652-b69e-c190f0c140fe/GCF_010731775.1_ASM1073177v1_genomic.fna.gz --refList GCF_010731775.1_ASM1073177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731775.1_ASM1073177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:30,418] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:30,437] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:30,437] [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_010731775.1	s__Mycobacterium mantenii	100.0	2061	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	conclusive
GCF_001665835.1	s__Mycobacterium colombiense_A	89.9502	1540	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	89.8333	1547	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001672755.1	s__Mycobacterium colombiense_C	89.7416	1529	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	89.6737	1604	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665875.1	s__Mycobacterium sp001665875	89.5931	1489	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	89.4656	1556	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_003284975.1	s__Mycobacterium europaeum_A	88.7077	1417	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001667145.1	s__Mycobacterium sp001667145	88.4633	1419	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086125.1	s__Mycobacterium arosiense	88.2605	1413	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672975.1	s__Mycobacterium sp001672975	88.0481	1444	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	87.0266	1422	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731675.1	s__Mycobacterium marseillense	86.7197	1491	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_002102255.1	s__Mycobacterium nebraskense	84.4386	1444	2061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:30,439] [INFO] GTDB search result was written to GCF_010731775.1_ASM1073177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:30,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:30,443] [INFO] DFAST_QC result json was written to GCF_010731775.1_ASM1073177v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:30,443] [INFO] DFAST_QC completed!
[2024-01-24 14:15:30,443] [INFO] Total running time: 0h2m12s