[2024-01-24 13:31:26,007] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,008] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference
[2024-01-24 13:31:27,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,204] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg41c905c8-d620-4167-992c-5284c4ee8559/GCF_008806775.1_ASM880677v1_genomic.fna.gz | prodigal -d GCF_008806775.1_ASM880677v1_genomic.fna/cds.fna -a GCF_008806775.1_ASM880677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:38,349] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:38,349] [INFO] Task started: HMMsearch
[2024-01-24 13:31:38,350] [INFO] Running command: hmmsearch --tblout GCF_008806775.1_ASM880677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/reference_markers.hmm GCF_008806775.1_ASM880677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:38,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:38,623] [INFO] Found 6/6 markers.
[2024-01-24 13:31:38,655] [INFO] Query marker FASTA was written to GCF_008806775.1_ASM880677v1_genomic.fna/markers.fasta
[2024-01-24 13:31:38,655] [INFO] Task started: Blastn
[2024-01-24 13:31:38,655] [INFO] Running command: blastn -query GCF_008806775.1_ASM880677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/reference_markers.fasta -out GCF_008806775.1_ASM880677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:39,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:39,350] [INFO] Selected 30 target genomes.
[2024-01-24 13:31:39,350] [INFO] Target genome list was writen to GCF_008806775.1_ASM880677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:39,655] [INFO] Task started: fastANI
[2024-01-24 13:31:39,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c905c8-d620-4167-992c-5284c4ee8559/GCF_008806775.1_ASM880677v1_genomic.fna.gz --refList GCF_008806775.1_ASM880677v1_genomic.fna/target_genomes.txt --output GCF_008806775.1_ASM880677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,850] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:58,850] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,850] [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 luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	100.0	1118	1119	95	conclusive
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	79.5104	458	1119	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	78.9382	336	1119	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	78.9232	339	1119	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	78.5737	288	1119	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	78.4622	304	1119	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	78.3893	295	1119	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	78.3443	299	1119	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	78.3429	286	1119	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	78.3046	286	1119	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.3017	315	1119	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.2576	307	1119	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.2235	304	1119	95	below_threshold
Flavobacterium psychrophilum	strain=ATCC 49418	GCA_002217405.1	96345	96345	type	True	78.1593	235	1119	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	78.1421	264	1119	95	below_threshold
Flavobacterium psychrophilum	strain=FPG3	GCA_000754405.1	96345	96345	type	True	78.1339	238	1119	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	78.1249	265	1119	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	78.1061	266	1119	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.0748	280	1119	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	78.0639	280	1119	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	78.0626	277	1119	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	78.0542	282	1119	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	78.0415	277	1119	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.0147	254	1119	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	77.9748	278	1119	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.7324	243	1119	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.5418	180	1119	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.1909	85	1119	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1625	88	1119	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	76.0776	52	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,854] [INFO] DFAST Taxonomy check result was written to GCF_008806775.1_ASM880677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/checkm_data
[2024-01-24 13:31:58,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,895] [INFO] Task started: CheckM
[2024-01-24 13:31:58,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008806775.1_ASM880677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008806775.1_ASM880677v1_genomic.fna/checkm_input GCF_008806775.1_ASM880677v1_genomic.fna/checkm_result
[2024-01-24 13:32:35,277] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:35,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:35,302] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:35,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:35,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008806775.1_ASM880677v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:35,303] [INFO] Task started: Blastn
[2024-01-24 13:32:35,304] [INFO] Running command: blastn -query GCF_008806775.1_ASM880677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4ebd6a-3f49-49d6-9cdd-837b9b9e10d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008806775.1_ASM880677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:36,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:36,287] [INFO] Selected 25 target genomes.
[2024-01-24 13:32:36,288] [INFO] Target genome list was writen to GCF_008806775.1_ASM880677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:36,466] [INFO] Task started: fastANI
[2024-01-24 13:32:36,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c905c8-d620-4167-992c-5284c4ee8559/GCF_008806775.1_ASM880677v1_genomic.fna.gz --refList GCF_008806775.1_ASM880677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008806775.1_ASM880677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:53,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:53,090] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:53,090] [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_008806775.1	s__Flavobacterium luteum	100.0	1118	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016718345.1	s__Flavobacterium sp016718345	79.607	466	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	79.4994	459	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	78.9445	336	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_007097265.1	s__Flavobacterium gawalongense	78.9163	340	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_003634825.1	s__Flavobacterium sp003634825	78.794	352	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744835.1	s__Flavobacterium sp000744835	78.7595	355	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099915.1	s__Flavobacterium omnivorum	78.5926	287	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	78.4979	321	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_002754315.1	s__Flavobacterium sp002754315	78.4948	344	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_004349135.1	s__Flavobacterium sandaracinum	78.4736	303	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	78.4614	333	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	78.3839	294	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_002813295.1	s__Flavobacterium sp002813295	78.1721	332	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217405.1	s__Flavobacterium psychrophilum	78.1593	235	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.22	98.91	0.92	0.83	157	-
GCF_002797935.1	s__Flavobacterium sp002797935	78.1309	298	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217435.1	s__Flavobacterium reichenbachii	78.1063	267	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_004362665.1	s__Flavobacterium dankookense	78.0618	281	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789235.1	s__Flavobacterium sp009789235	78.0372	278	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	77.977	279	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.9158	278	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	77.8778	267	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	77.8548	291	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_903837025.1	s__Flavobacterium sp903837025	77.8154	225	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581925.1	s__Gelidibacter sp017581925	76.0776	52	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,092] [INFO] GTDB search result was written to GCF_008806775.1_ASM880677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:53,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:53,098] [INFO] DFAST_QC result json was written to GCF_008806775.1_ASM880677v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:53,099] [INFO] DFAST_QC completed!
[2024-01-24 13:32:53,099] [INFO] Total running time: 0h1m27s