[2024-01-24 13:22:25,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference
[2024-01-24 13:22:26,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,679] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg8514e1c3-ced5-42e1-8e3e-ac03ac11fd32/GCF_010731855.1_ASM1073185v1_genomic.fna.gz | prodigal -d GCF_010731855.1_ASM1073185v1_genomic.fna/cds.fna -a GCF_010731855.1_ASM1073185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:45,177] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:45,177] [INFO] Task started: HMMsearch
[2024-01-24 13:22:45,177] [INFO] Running command: hmmsearch --tblout GCF_010731855.1_ASM1073185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/reference_markers.hmm GCF_010731855.1_ASM1073185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:45,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:45,519] [INFO] Found 6/6 markers.
[2024-01-24 13:22:45,566] [INFO] Query marker FASTA was written to GCF_010731855.1_ASM1073185v1_genomic.fna/markers.fasta
[2024-01-24 13:22:45,566] [INFO] Task started: Blastn
[2024-01-24 13:22:45,566] [INFO] Running command: blastn -query GCF_010731855.1_ASM1073185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/reference_markers.fasta -out GCF_010731855.1_ASM1073185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:46,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:46,791] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:46,792] [INFO] Target genome list was writen to GCF_010731855.1_ASM1073185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:46,815] [INFO] Task started: fastANI
[2024-01-24 13:22:46,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg8514e1c3-ced5-42e1-8e3e-ac03ac11fd32/GCF_010731855.1_ASM1073185v1_genomic.fna.gz --refList GCF_010731855.1_ASM1073185v1_genomic.fna/target_genomes.txt --output GCF_010731855.1_ASM1073185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:06,045] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:06,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:06,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:06,055] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:06,055] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:06,055] [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
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	100.0	1898	1898	95	conclusive
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	83.3228	884	1898	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	82.0761	1126	1898	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	81.9356	1153	1898	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	81.9108	1151	1898	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	81.8757	1168	1898	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	81.7807	1164	1898	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	81.6691	1162	1898	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	81.5396	1177	1898	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	81.5266	1106	1898	95	below_threshold
Mycolicibacterium sarraceniae	strain=JCM 30395	GCA_010731875.1	1534348	1534348	type	True	81.3522	1012	1898	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	80.0173	841	1898	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	79.5111	754	1898	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.5024	787	1898	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	79.0287	689	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:06,057] [INFO] DFAST Taxonomy check result was written to GCF_010731855.1_ASM1073185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:06,058] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:06,058] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:06,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/checkm_data
[2024-01-24 13:23:06,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:06,112] [INFO] Task started: CheckM
[2024-01-24 13:23:06,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731855.1_ASM1073185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731855.1_ASM1073185v1_genomic.fna/checkm_input GCF_010731855.1_ASM1073185v1_genomic.fna/checkm_result
[2024-01-24 13:24:14,681] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:14,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:14,698] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:14,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:14,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731855.1_ASM1073185v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:14,698] [INFO] Task started: Blastn
[2024-01-24 13:24:14,699] [INFO] Running command: blastn -query GCF_010731855.1_ASM1073185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcceb6cd-6488-488b-83f4-7b8233224e05/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731855.1_ASM1073185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:16,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:16,443] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:16,443] [INFO] Target genome list was writen to GCF_010731855.1_ASM1073185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:16,452] [INFO] Task started: fastANI
[2024-01-24 13:24:16,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg8514e1c3-ced5-42e1-8e3e-ac03ac11fd32/GCF_010731855.1_ASM1073185v1_genomic.fna.gz --refList GCF_010731855.1_ASM1073185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731855.1_ASM1073185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:38,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:38,148] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:38,148] [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_010731855.1	s__Mycobacterium anyangense	100.0	1898	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001494595.1	s__Mycobacterium sp001494595	87.2881	1463	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694515.1	s__Mycobacterium sp011694515	85.1938	1330	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	82.7432	1245	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007745.1	s__Mycobacterium litorale_A	82.4441	1222	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745805.1	s__Mycobacterium sp004745805	82.1843	1224	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	82.1636	1119	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_002887815.1	s__Mycobacterium sp002887815	81.9228	1167	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	81.8917	1171	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_013337765.1	s__Mycobacterium sp003053865	81.8008	1150	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCA_900078375.1	s__Mycobacterium sp900078375	81.7034	1143	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404075.1	s__Mycobacterium sp013404075	81.6587	1162	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250655.1	s__Mycobacterium sphagni	81.5307	1106	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731875.1	s__Mycobacterium sarraceniae	81.3572	1011	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096635.1	s__Mycobacterium sp007096635	79.8225	800	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	79.8041	823	1898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:38,149] [INFO] GTDB search result was written to GCF_010731855.1_ASM1073185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:38,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:38,153] [INFO] DFAST_QC result json was written to GCF_010731855.1_ASM1073185v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:38,153] [INFO] DFAST_QC completed!
[2024-01-24 13:24:38,153] [INFO] Total running time: 0h2m13s