[2024-01-24 13:25:29,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,371] [INFO] DQC Reference Directory: /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference
[2024-01-24 13:25:30,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,743] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg127c2b33-7eeb-430e-bc06-bf77db9ab897/GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna.gz | prodigal -d GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/cds.fna -a GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:52,534] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:52,535] [INFO] Task started: HMMsearch
[2024-01-24 13:25:52,535] [INFO] Running command: hmmsearch --tblout GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/reference_markers.hmm GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:52,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:52,864] [INFO] Found 6/6 markers.
[2024-01-24 13:25:52,922] [INFO] Query marker FASTA was written to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/markers.fasta
[2024-01-24 13:25:52,922] [INFO] Task started: Blastn
[2024-01-24 13:25:52,922] [INFO] Running command: blastn -query GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/reference_markers.fasta -out GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:54,289] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:54,293] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:54,293] [INFO] Target genome list was writen to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:54,296] [INFO] Task started: fastANI
[2024-01-24 13:25:54,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg127c2b33-7eeb-430e-bc06-bf77db9ab897/GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna.gz --refList GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/target_genomes.txt --output GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:11,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:11,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:11,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:11,725] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:11,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:11,725] [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 cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	100.0	2150	2151	95	conclusive
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	99.9847	2128	2151	95	conclusive
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	92.8795	1698	2151	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	92.8243	1684	2151	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	84.8967	1470	2151	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	81.9883	1192	2151	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.6617	803	2151	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.5946	794	2151	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.2174	909	2151	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.0636	925	2151	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.899	968	2151	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.8137	898	2151	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.4027	915	2151	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:11,727] [INFO] DFAST Taxonomy check result was written to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:11,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:11,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:11,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/checkm_data
[2024-01-24 13:26:11,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:11,788] [INFO] Task started: CheckM
[2024-01-24 13:26:11,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/checkm_input GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/checkm_result
[2024-01-24 13:27:30,645] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:30,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:30,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:30,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:30,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 13:27:30,669] [INFO] Task started: Blastn
[2024-01-24 13:27:30,669] [INFO] Running command: blastn -query GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6dbf298-128b-4b36-94a4-ce1f212d15f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:32,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:32,831] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:32,831] [INFO] Target genome list was writen to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:32,901] [INFO] Task started: fastANI
[2024-01-24 13:27:32,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg127c2b33-7eeb-430e-bc06-bf77db9ab897/GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna.gz --refList GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:57,657] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:57,674] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:57,675] [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_000613185.1	s__Mycobacterium cosmeticum	100.0	2150	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	conclusive
GCF_002101555.1	s__Mycobacterium canariasense	92.8228	1684	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011758805.1	s__Mycobacterium fluoranthenivorans	84.9276	1465	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	-
GCA_016197365.1	s__Mycobacterium cosmeticum_A	84.7736	1338	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078775.1	s__Mycobacterium aurum_A	82.288	1183	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086115.1	s__Mycobacterium bacteremicum	81.9634	1196	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	81.9319	1149	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	81.7401	1199	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCA_011620645.1	s__Mycobacterium sp011620645	81.6603	784	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	81.2623	1061	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_001245615.1	s__Mycobacterium neworleansense	80.8628	1079	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.6864	1015	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726955.1	s__Mycobacterium fallax	80.6555	800	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.6142	864	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382405.1	s__Mycobacterium sp000382405	80.2075	762	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	80.2065	1036	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_010729895.1	s__Mycobacterium confluentis	80.0272	924	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002591975.1	s__Mycobacterium neglectum	79.1525	823	2151	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:57,678] [INFO] GTDB search result was written to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:57,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:57,682] [INFO] DFAST_QC result json was written to GCF_000613185.1_PRJEB5748_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 13:27:57,682] [INFO] DFAST_QC completed!
[2024-01-24 13:27:57,683] [INFO] Total running time: 0h2m28s