[2024-01-24 13:49:27,688] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference
[2024-01-24 13:49:28,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,987] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgab8e5944-c090-4166-a9bc-765bd48706a0/GCF_005670605.1_ASM567060v1_genomic.fna.gz | prodigal -d GCF_005670605.1_ASM567060v1_genomic.fna/cds.fna -a GCF_005670605.1_ASM567060v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,413] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,414] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,414] [INFO] Running command: hmmsearch --tblout GCF_005670605.1_ASM567060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/reference_markers.hmm GCF_005670605.1_ASM567060v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:47,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:47,716] [INFO] Found 6/6 markers.
[2024-01-24 13:49:47,765] [INFO] Query marker FASTA was written to GCF_005670605.1_ASM567060v1_genomic.fna/markers.fasta
[2024-01-24 13:49:47,765] [INFO] Task started: Blastn
[2024-01-24 13:49:47,766] [INFO] Running command: blastn -query GCF_005670605.1_ASM567060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/reference_markers.fasta -out GCF_005670605.1_ASM567060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,977] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:48,978] [INFO] Target genome list was writen to GCF_005670605.1_ASM567060v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:48,985] [INFO] Task started: fastANI
[2024-01-24 13:49:48,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8e5944-c090-4166-a9bc-765bd48706a0/GCF_005670605.1_ASM567060v1_genomic.fna.gz --refList GCF_005670605.1_ASM567060v1_genomic.fna/target_genomes.txt --output GCF_005670605.1_ASM567060v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:09,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:09,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:09,254] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:09,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:09,254] [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 neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	100.0	1811	1814	95	conclusive
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	99.9933	1790	1814	95	conclusive
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_000724065.1	1795	1795	type	True	99.9416	1800	1814	95	conclusive
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	85.464	1409	1814	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	81.4578	1083	1814	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	81.1447	1015	1814	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	80.7979	1027	1814	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	79.9151	917	1814	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.8626	837	1814	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	79.848	889	1814	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.3576	745	1814	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.232	730	1814	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.1601	740	1814	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.1419	756	1814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,264] [INFO] DFAST Taxonomy check result was written to GCF_005670605.1_ASM567060v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:09,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:09,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:09,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/checkm_data
[2024-01-24 13:50:09,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:09,324] [INFO] Task started: CheckM
[2024-01-24 13:50:09,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005670605.1_ASM567060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005670605.1_ASM567060v1_genomic.fna/checkm_input GCF_005670605.1_ASM567060v1_genomic.fna/checkm_result
[2024-01-24 13:51:11,109] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:11,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:11,134] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:11,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:11,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005670605.1_ASM567060v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:11,135] [INFO] Task started: Blastn
[2024-01-24 13:51:11,136] [INFO] Running command: blastn -query GCF_005670605.1_ASM567060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd015ddd9-9345-4351-9ffc-3c7859233f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_005670605.1_ASM567060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:12,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:12,843] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:12,843] [INFO] Target genome list was writen to GCF_005670605.1_ASM567060v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:12,873] [INFO] Task started: fastANI
[2024-01-24 13:51:12,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8e5944-c090-4166-a9bc-765bd48706a0/GCF_005670605.1_ASM567060v1_genomic.fna.gz --refList GCF_005670605.1_ASM567060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005670605.1_ASM567060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:28,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:28,742] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:28,743] [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_000691525.1	s__Mycobacterium neoaurum	99.9933	1790	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	98.36	0.96	0.91	6	conclusive
GCF_000317305.3	s__Mycobacterium neoaurum_A	92.968	1573	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_002086115.1	s__Mycobacterium bacteremicum	85.4563	1410	1814	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	82.5077	1198	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	82.4084	1231	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_001428895.1	s__Mycobacterium sp001428895	82.3295	1290	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329585.1	s__Mycobacterium sp008329585	82.2918	1233	1814	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	82.1433	1182	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_000613185.1	s__Mycobacterium cosmeticum	81.4438	1098	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002101555.1	s__Mycobacterium canariasense	81.106	1021	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900078665.2	s__Mycobacterium houstonense	79.9869	880	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	77.5692	375	1814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:28,744] [INFO] GTDB search result was written to GCF_005670605.1_ASM567060v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:28,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:28,748] [INFO] DFAST_QC result json was written to GCF_005670605.1_ASM567060v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:28,749] [INFO] DFAST_QC completed!
[2024-01-24 13:51:28,749] [INFO] Total running time: 0h2m1s