[2024-01-25 18:15:20,627] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference
[2024-01-25 18:15:21,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:21,780] [INFO] Task started: Prodigal
[2024-01-25 18:15:21,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg46939710-f60a-477c-b733-687b992fe301/GCF_002101735.1_ASM210173v1_genomic.fna.gz | prodigal -d GCF_002101735.1_ASM210173v1_genomic.fna/cds.fna -a GCF_002101735.1_ASM210173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:39,744] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:39,745] [INFO] Task started: HMMsearch
[2024-01-25 18:15:39,745] [INFO] Running command: hmmsearch --tblout GCF_002101735.1_ASM210173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/reference_markers.hmm GCF_002101735.1_ASM210173v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:40,033] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:40,034] [INFO] Found 6/6 markers.
[2024-01-25 18:15:40,079] [INFO] Query marker FASTA was written to GCF_002101735.1_ASM210173v1_genomic.fna/markers.fasta
[2024-01-25 18:15:40,079] [INFO] Task started: Blastn
[2024-01-25 18:15:40,079] [INFO] Running command: blastn -query GCF_002101735.1_ASM210173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/reference_markers.fasta -out GCF_002101735.1_ASM210173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:41,158] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:41,162] [INFO] Selected 17 target genomes.
[2024-01-25 18:15:41,162] [INFO] Target genome list was writen to GCF_002101735.1_ASM210173v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:41,169] [INFO] Task started: fastANI
[2024-01-25 18:15:41,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg46939710-f60a-477c-b733-687b992fe301/GCF_002101735.1_ASM210173v1_genomic.fna.gz --refList GCF_002101735.1_ASM210173v1_genomic.fna/target_genomes.txt --output GCF_002101735.1_ASM210173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:00,759] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:00,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:00,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:00,770] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:16:00,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:00,770] [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 kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	100.0	1772	1778	95	conclusive
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	99.784	1580	1778	95	conclusive
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	90.8389	1380	1778	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	90.8229	1391	1778	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	90.5168	1345	1778	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	90.1181	1033	1778	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	82.9077	1099	1778	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	82.1024	1060	1778	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	81.857	1009	1778	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	81.8517	1053	1778	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	81.5861	995	1778	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	81.586	994	1778	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	81.2224	972	1778	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	80.1031	776	1778	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	80.0978	796	1778	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	79.9283	710	1778	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	79.7008	739	1778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:00,772] [INFO] DFAST Taxonomy check result was written to GCF_002101735.1_ASM210173v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:00,772] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:00,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:00,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/checkm_data
[2024-01-25 18:16:00,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:00,825] [INFO] Task started: CheckM
[2024-01-25 18:16:00,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101735.1_ASM210173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101735.1_ASM210173v1_genomic.fna/checkm_input GCF_002101735.1_ASM210173v1_genomic.fna/checkm_result
[2024-01-25 18:16:51,858] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:51,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:51,886] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:51,886] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:51,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101735.1_ASM210173v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:51,887] [INFO] Task started: Blastn
[2024-01-25 18:16:51,887] [INFO] Running command: blastn -query GCF_002101735.1_ASM210173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0027ba-9df0-4f6a-a2fd-67f2b43dea07/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101735.1_ASM210173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:53,514] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:53,517] [INFO] Selected 20 target genomes.
[2024-01-25 18:16:53,518] [INFO] Target genome list was writen to GCF_002101735.1_ASM210173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:53,534] [INFO] Task started: fastANI
[2024-01-25 18:16:53,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg46939710-f60a-477c-b733-687b992fe301/GCF_002101735.1_ASM210173v1_genomic.fna.gz --refList GCF_002101735.1_ASM210173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101735.1_ASM210173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:18,019] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:18,031] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:18,031] [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_002101735.1	s__Mycobacterium kyorinense	100.0	1772	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	conclusive
GCF_010728725.1	s__Mycobacterium branderi	90.8348	1390	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003402475.1	s__Mycobacterium sp003402475	90.6939	1361	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101595.1	s__Mycobacterium celatum	90.5168	1345	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001672775.1	s__Mycobacterium kyorinense_A	83.0791	1093	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102185.1	s__Mycobacterium fragae	82.9179	1098	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101905.1	s__Mycobacterium shimoidei	82.8518	1037	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	-
GCA_004354905.1	s__Mycobacterium eburneum	81.8575	1015	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_010731635.1	s__Mycobacterium noviomagense	81.8371	1055	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	81.5136	939	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCA_008709575.1	s__Mycobacterium sp008709575	81.4947	776	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	81.4115	987	1778	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	81.3713	950	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592155.1	s__Mycobacterium heckeshornense	81.2177	972	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_900240975.1	s__Mycobacterium sp900240975	80.9153	975	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001666835.1	s__Mycobacterium sp001666835	80.6768	918	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_900603025.1	s__Mycobacterium hassiacum	80.1136	811	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000195955.2	s__Mycobacterium tuberculosis	79.6928	741	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_001499905.1	s__Mycobacterium sp001499905	79.5424	711	1778	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	79.2289	717	1778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:18,033] [INFO] GTDB search result was written to GCF_002101735.1_ASM210173v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:18,033] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:18,037] [INFO] DFAST_QC result json was written to GCF_002101735.1_ASM210173v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:18,037] [INFO] DFAST_QC completed!
[2024-01-25 18:17:18,037] [INFO] Total running time: 0h1m57s