[2024-01-24 14:12:45,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference
[2024-01-24 14:12:47,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,067] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b8631d6-3890-4c36-8a7d-ba242a7851b8/GCF_000419685.1_ASM41968v1_genomic.fna.gz | prodigal -d GCF_000419685.1_ASM41968v1_genomic.fna/cds.fna -a GCF_000419685.1_ASM41968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:59,537] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:59,537] [INFO] Task started: HMMsearch
[2024-01-24 14:12:59,537] [INFO] Running command: hmmsearch --tblout GCF_000419685.1_ASM41968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/reference_markers.hmm GCF_000419685.1_ASM41968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:59,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:59,822] [INFO] Found 6/6 markers.
[2024-01-24 14:12:59,859] [INFO] Query marker FASTA was written to GCF_000419685.1_ASM41968v1_genomic.fna/markers.fasta
[2024-01-24 14:12:59,860] [INFO] Task started: Blastn
[2024-01-24 14:12:59,860] [INFO] Running command: blastn -query GCF_000419685.1_ASM41968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/reference_markers.fasta -out GCF_000419685.1_ASM41968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:00,607] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:00,611] [INFO] Selected 24 target genomes.
[2024-01-24 14:13:00,611] [INFO] Target genome list was writen to GCF_000419685.1_ASM41968v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:00,622] [INFO] Task started: fastANI
[2024-01-24 14:13:00,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b8631d6-3890-4c36-8a7d-ba242a7851b8/GCF_000419685.1_ASM41968v1_genomic.fna.gz --refList GCF_000419685.1_ASM41968v1_genomic.fna/target_genomes.txt --output GCF_000419685.1_ASM41968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:16,364] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:16,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:16,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:16,390] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:16,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:16,391] [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
Flavobacterium antarcticum	strain=DSM 19726	GCA_000419685.1	271155	271155	type	True	100.0	1019	1020	95	conclusive
Flavobacterium tegetincola	strain=DSM 22377	GCA_000425485.1	150172	150172	type	True	82.1714	626	1020	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	78.7448	314	1020	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	78.214	221	1020	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	78.1923	218	1020	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	78.0578	220	1020	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	78.0496	165	1020	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	78.0392	223	1020	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	77.9803	229	1020	95	below_threshold
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	77.94	173	1020	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	77.9381	192	1020	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.9289	197	1020	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	77.9069	202	1020	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	77.905	189	1020	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	77.8692	187	1020	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	77.8416	184	1020	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.7937	207	1020	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	77.7503	223	1020	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.742	206	1020	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	77.7104	214	1020	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3309	203	1020	95	below_threshold
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	77.2371	198	1020	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.1444	154	1020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:16,392] [INFO] DFAST Taxonomy check result was written to GCF_000419685.1_ASM41968v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:16,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:16,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:16,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/checkm_data
[2024-01-24 14:13:16,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:16,428] [INFO] Task started: CheckM
[2024-01-24 14:13:16,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000419685.1_ASM41968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000419685.1_ASM41968v1_genomic.fna/checkm_input GCF_000419685.1_ASM41968v1_genomic.fna/checkm_result
[2024-01-24 14:13:56,650] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:56,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:56,685] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:56,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:56,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000419685.1_ASM41968v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:56,687] [INFO] Task started: Blastn
[2024-01-24 14:13:56,687] [INFO] Running command: blastn -query GCF_000419685.1_ASM41968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg168e764a-f7a2-4305-acb7-aa64b9e6ad81/dqc_reference/reference_markers_gtdb.fasta -out GCF_000419685.1_ASM41968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:57,708] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:57,716] [INFO] Selected 22 target genomes.
[2024-01-24 14:13:57,717] [INFO] Target genome list was writen to GCF_000419685.1_ASM41968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:57,755] [INFO] Task started: fastANI
[2024-01-24 14:13:57,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b8631d6-3890-4c36-8a7d-ba242a7851b8/GCF_000419685.1_ASM41968v1_genomic.fna.gz --refList GCF_000419685.1_ASM41968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000419685.1_ASM41968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:15,731] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:15,756] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:15,757] [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_000419685.1	s__Flavobacterium antarcticum	100.0	1019	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425485.1	s__Flavobacterium tegetincola	82.1634	627	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.7483	315	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	78.2823	233	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975985.1	s__Flavobacterium sp001975985	78.2176	207	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	78.2068	199	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	78.1923	218	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076455.1	s__Flavobacterium faecale	78.0618	166	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001529295.1	s__Flavobacterium sp001529295	78.0431	230	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	78.034	223	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	77.9116	198	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129545.1	s__Flavobacterium fluvii	77.9045	197	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	77.8991	190	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129705.1	s__Flavobacterium granuli	77.8288	186	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007097265.1	s__Flavobacterium gawalongense	77.76	224	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_004339525.1	s__Flavobacterium sp004339525	77.716	239	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900143245.1	s__Flavobacterium fryxellicola	77.6767	219	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009495755.1	s__Flavobacterium sp009495755	77.623	209	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	77.5436	211	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCF_003268815.1	s__Flavobacterium lacus	77.2241	199	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	77.0475	171	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	76.8596	173	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:15,759] [INFO] GTDB search result was written to GCF_000419685.1_ASM41968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:15,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:15,767] [INFO] DFAST_QC result json was written to GCF_000419685.1_ASM41968v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:15,767] [INFO] DFAST_QC completed!
[2024-01-24 14:14:15,767] [INFO] Total running time: 0h1m30s