[2023-06-27 04:25:05,325] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:25:05,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:25:05,328] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference
[2023-06-27 04:25:07,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:25:07,097] [INFO] Task started: Prodigal
[2023-06-27 04:25:07,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg91ad4e88-d44b-4e1a-a96b-1dd115d45438/GCA_026393235.1_ASM2639323v1_genomic.fna.gz | prodigal -d GCA_026393235.1_ASM2639323v1_genomic.fna/cds.fna -a GCA_026393235.1_ASM2639323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:25:16,307] [INFO] Task succeeded: Prodigal
[2023-06-27 04:25:16,308] [INFO] Task started: HMMsearch
[2023-06-27 04:25:16,309] [INFO] Running command: hmmsearch --tblout GCA_026393235.1_ASM2639323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/reference_markers.hmm GCA_026393235.1_ASM2639323v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:25:16,555] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:25:16,557] [INFO] Found 6/6 markers.
[2023-06-27 04:25:16,610] [INFO] Query marker FASTA was written to GCA_026393235.1_ASM2639323v1_genomic.fna/markers.fasta
[2023-06-27 04:25:16,610] [INFO] Task started: Blastn
[2023-06-27 04:25:16,611] [INFO] Running command: blastn -query GCA_026393235.1_ASM2639323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/reference_markers.fasta -out GCA_026393235.1_ASM2639323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:25:17,731] [INFO] Task succeeded: Blastn
[2023-06-27 04:25:17,736] [INFO] Selected 22 target genomes.
[2023-06-27 04:25:17,737] [INFO] Target genome list was writen to GCA_026393235.1_ASM2639323v1_genomic.fna/target_genomes.txt
[2023-06-27 04:25:17,753] [INFO] Task started: fastANI
[2023-06-27 04:25:17,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ad4e88-d44b-4e1a-a96b-1dd115d45438/GCA_026393235.1_ASM2639323v1_genomic.fna.gz --refList GCA_026393235.1_ASM2639323v1_genomic.fna/target_genomes.txt --output GCA_026393235.1_ASM2639323v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:25:38,551] [INFO] Task succeeded: fastANI
[2023-06-27 04:25:38,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:25:38,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:25:38,581] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:25:38,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 04:25:38,581] [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
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.4252	504	972	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.2053	588	972	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.978	543	972	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.942	523	972	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	78.8935	535	972	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	78.8374	440	972	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	78.8208	441	972	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	78.8136	543	972	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	78.7792	543	972	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	78.7365	392	972	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	78.719	390	972	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	78.6893	520	972	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	78.5867	542	972	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	78.4566	464	972	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	78.4184	469	972	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	78.3084	408	972	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	78.2921	407	972	95	below_threshold
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	78.2801	457	972	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	78.2429	451	972	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	78.211	369	972	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	78.2108	427	972	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	78.1319	418	972	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:25:38,583] [INFO] DFAST Taxonomy check result was written to GCA_026393235.1_ASM2639323v1_genomic.fna/tc_result.tsv
[2023-06-27 04:25:38,584] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:25:38,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:25:38,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/checkm_data
[2023-06-27 04:25:38,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:25:38,625] [INFO] Task started: CheckM
[2023-06-27 04:25:38,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026393235.1_ASM2639323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026393235.1_ASM2639323v1_genomic.fna/checkm_input GCA_026393235.1_ASM2639323v1_genomic.fna/checkm_result
[2023-06-27 04:26:10,505] [INFO] Task succeeded: CheckM
[2023-06-27 04:26:10,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:26:10,572] [INFO] ===== Completeness check finished =====
[2023-06-27 04:26:10,572] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:26:10,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026393235.1_ASM2639323v1_genomic.fna/markers.fasta)
[2023-06-27 04:26:10,573] [INFO] Task started: Blastn
[2023-06-27 04:26:10,573] [INFO] Running command: blastn -query GCA_026393235.1_ASM2639323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5762b91-1d65-4bad-a3ab-fe19b2d07f6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_026393235.1_ASM2639323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:26:12,187] [INFO] Task succeeded: Blastn
[2023-06-27 04:26:12,198] [INFO] Selected 18 target genomes.
[2023-06-27 04:26:12,198] [INFO] Target genome list was writen to GCA_026393235.1_ASM2639323v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:26:12,209] [INFO] Task started: fastANI
[2023-06-27 04:26:12,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg91ad4e88-d44b-4e1a-a96b-1dd115d45438/GCA_026393235.1_ASM2639323v1_genomic.fna.gz --refList GCA_026393235.1_ASM2639323v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026393235.1_ASM2639323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:26:26,722] [INFO] Task succeeded: fastANI
[2023-06-27 04:26:26,749] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:26:26,749] [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
GCA_903911165.1	s__Mycobacterium sp903911165	98.183	688	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005789055.1	s__Mycobacterium sp005789055	90.531	455	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401645.1	s__Mycobacterium sp018401645	82.949	676	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462945.1	s__Mycobacterium sp016462945	82.151	706	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	80.283	548	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	79.9368	616	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_001510415.1	s__Mycobacterium sp001510415	79.8022	348	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862565.1	s__Mycobacterium sp903862565	79.647	516	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877095.1	s__Mycobacterium sp903877095	79.582	590	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_018883075.1	s__Mycobacterium sp018883075	79.5589	442	972	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	79.273	575	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882965.1	s__Mycobacterium sp018882965	79.2654	535	972	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	79.2605	548	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731855.1	s__Mycobacterium anyangense	79.2092	588	972	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	79.0655	559	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	78.6036	541	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	78.2914	471	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:26:26,751] [INFO] GTDB search result was written to GCA_026393235.1_ASM2639323v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:26:26,752] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:26:26,756] [INFO] DFAST_QC result json was written to GCA_026393235.1_ASM2639323v1_genomic.fna/dqc_result.json
[2023-06-27 04:26:26,756] [INFO] DFAST_QC completed!
[2023-06-27 04:26:26,756] [INFO] Total running time: 0h1m21s