[2024-01-24 13:32:40,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:40,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:40,428] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference
[2024-01-24 13:32:41,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:41,817] [INFO] Task started: Prodigal
[2024-01-24 13:32:41,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg81d31ff3-81df-4121-b7d8-b3287cdac7f5/GCF_007714205.1_ASM771420v1_genomic.fna.gz | prodigal -d GCF_007714205.1_ASM771420v1_genomic.fna/cds.fna -a GCF_007714205.1_ASM771420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:58,749] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:58,749] [INFO] Task started: HMMsearch
[2024-01-24 13:32:58,749] [INFO] Running command: hmmsearch --tblout GCF_007714205.1_ASM771420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/reference_markers.hmm GCF_007714205.1_ASM771420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:59,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:59,048] [INFO] Found 6/6 markers.
[2024-01-24 13:32:59,102] [INFO] Query marker FASTA was written to GCF_007714205.1_ASM771420v1_genomic.fna/markers.fasta
[2024-01-24 13:32:59,103] [INFO] Task started: Blastn
[2024-01-24 13:32:59,103] [INFO] Running command: blastn -query GCF_007714205.1_ASM771420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/reference_markers.fasta -out GCF_007714205.1_ASM771420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:00,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:00,311] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:00,312] [INFO] Target genome list was writen to GCF_007714205.1_ASM771420v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:00,415] [INFO] Task started: fastANI
[2024-01-24 13:33:00,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d31ff3-81df-4121-b7d8-b3287cdac7f5/GCF_007714205.1_ASM771420v1_genomic.fna.gz --refList GCF_007714205.1_ASM771420v1_genomic.fna/target_genomes.txt --output GCF_007714205.1_ASM771420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:20,088] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:20,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:20,108] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:20,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:20,108] [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 helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	100.0	1740	1752	95	conclusive
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	84.5462	1235	1752	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	84.506	1248	1752	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	84.3171	1055	1752	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	84.3118	1068	1752	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	83.9027	1144	1752	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.5906	1089	1752	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.5673	1141	1752	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	83.4685	1115	1752	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	83.448	1094	1752	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.4205	1088	1752	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.4124	1089	1752	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	83.3751	1002	1752	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	80.9369	883	1752	95	below_threshold
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	80.8173	768	1752	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	80.8039	744	1752	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.6019	758	1752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,110] [INFO] DFAST Taxonomy check result was written to GCF_007714205.1_ASM771420v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:20,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:20,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:20,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/checkm_data
[2024-01-24 13:33:20,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:20,167] [INFO] Task started: CheckM
[2024-01-24 13:33:20,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007714205.1_ASM771420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007714205.1_ASM771420v1_genomic.fna/checkm_input GCF_007714205.1_ASM771420v1_genomic.fna/checkm_result
[2024-01-24 13:34:14,704] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:14,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:14,731] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:14,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:14,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007714205.1_ASM771420v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:14,733] [INFO] Task started: Blastn
[2024-01-24 13:34:14,733] [INFO] Running command: blastn -query GCF_007714205.1_ASM771420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e9505e-6fa9-4aba-81eb-c5533658d8ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_007714205.1_ASM771420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:16,484] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:16,489] [INFO] Selected 17 target genomes.
[2024-01-24 13:34:16,489] [INFO] Target genome list was writen to GCF_007714205.1_ASM771420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:16,663] [INFO] Task started: fastANI
[2024-01-24 13:34:16,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d31ff3-81df-4121-b7d8-b3287cdac7f5/GCF_007714205.1_ASM771420v1_genomic.fna.gz --refList GCF_007714205.1_ASM771420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007714205.1_ASM771420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:39,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:39,059] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:39,059] [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_007714205.1	s__Mycobacterium helveticum	100.0	1740	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_010730575.1	s__Mycobacterium parmense	84.5496	1242	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	84.3058	1069	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001668725.1	s__Mycobacterium sp001668725	83.9207	1103	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_002101815.1	s__Mycobacterium paraense	83.9126	1142	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	83.8606	1088	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	83.8428	1076	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.8426	1141	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	83.8166	1114	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667185.1	s__Mycobacterium sp001667185	83.752	1114	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	83.6621	1164	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001053185.1	s__Mycobacterium bohemicum	83.5871	1089	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_900078675.2	s__Mycobacterium interjectum	83.5841	1117	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667035.1	s__Mycobacterium sp001667035	83.5696	1038	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672815.1	s__Mycobacterium sp001672815	83.4768	1077	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667885.1	s__Mycobacterium scrofulaceum_C	83.1489	1059	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.31	98.31	0.93	0.93	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	80.9441	882	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:39,061] [INFO] GTDB search result was written to GCF_007714205.1_ASM771420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:39,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:39,069] [INFO] DFAST_QC result json was written to GCF_007714205.1_ASM771420v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:39,070] [INFO] DFAST_QC completed!
[2024-01-24 13:34:39,070] [INFO] Total running time: 0h1m59s