[2024-01-25 18:14:35,770] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:35,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:35,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference
[2024-01-25 18:14:36,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:36,916] [INFO] Task started: Prodigal
[2024-01-25 18:14:36,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg96213e15-0670-4cca-8e7d-34821fcb6be2/GCF_000735715.2_ASM73571v2_genomic.fna.gz | prodigal -d GCF_000735715.2_ASM73571v2_genomic.fna/cds.fna -a GCF_000735715.2_ASM73571v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:52,593] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:52,593] [INFO] Task started: HMMsearch
[2024-01-25 18:14:52,593] [INFO] Running command: hmmsearch --tblout GCF_000735715.2_ASM73571v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/reference_markers.hmm GCF_000735715.2_ASM73571v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:52,853] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:52,854] [INFO] Found 6/6 markers.
[2024-01-25 18:14:52,896] [INFO] Query marker FASTA was written to GCF_000735715.2_ASM73571v2_genomic.fna/markers.fasta
[2024-01-25 18:14:52,896] [INFO] Task started: Blastn
[2024-01-25 18:14:52,896] [INFO] Running command: blastn -query GCF_000735715.2_ASM73571v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/reference_markers.fasta -out GCF_000735715.2_ASM73571v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:53,562] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:53,565] [INFO] Selected 22 target genomes.
[2024-01-25 18:14:53,565] [INFO] Target genome list was writen to GCF_000735715.2_ASM73571v2_genomic.fna/target_genomes.txt
[2024-01-25 18:14:53,586] [INFO] Task started: fastANI
[2024-01-25 18:14:53,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg96213e15-0670-4cca-8e7d-34821fcb6be2/GCF_000735715.2_ASM73571v2_genomic.fna.gz --refList GCF_000735715.2_ASM73571v2_genomic.fna/target_genomes.txt --output GCF_000735715.2_ASM73571v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:18,732] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:18,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:18,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:18,745] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:18,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:18,746] [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 salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	95.2715	1546	1844	95	conclusive
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	87.3879	1273	1844	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	85.4872	1197	1844	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	85.3129	1181	1844	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	85.1986	1258	1844	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	85.153	1252	1844	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	84.8548	1062	1844	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.2477	1042	1844	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.1846	1052	1844	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	82.1212	935	1844	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	82.0463	955	1844	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	82.008	957	1844	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.9486	954	1844	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	81.819	930	1844	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	81.8162	941	1844	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	81.7835	837	1844	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	81.7473	933	1844	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.6289	852	1844	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.4241	909	1844	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.3935	919	1844	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.3179	945	1844	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.1864	177	1844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:18,747] [INFO] DFAST Taxonomy check result was written to GCF_000735715.2_ASM73571v2_genomic.fna/tc_result.tsv
[2024-01-25 18:15:18,748] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:18,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:18,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/checkm_data
[2024-01-25 18:15:18,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:18,803] [INFO] Task started: CheckM
[2024-01-25 18:15:18,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000735715.2_ASM73571v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000735715.2_ASM73571v2_genomic.fna/checkm_input GCF_000735715.2_ASM73571v2_genomic.fna/checkm_result
[2024-01-25 18:16:06,250] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:06,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:06,281] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:06,281] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:06,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000735715.2_ASM73571v2_genomic.fna/markers.fasta)
[2024-01-25 18:16:06,282] [INFO] Task started: Blastn
[2024-01-25 18:16:06,282] [INFO] Running command: blastn -query GCF_000735715.2_ASM73571v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg517002bc-c418-40e8-9f27-a7a2b934d7e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000735715.2_ASM73571v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:07,285] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:07,288] [INFO] Selected 18 target genomes.
[2024-01-25 18:16:07,288] [INFO] Target genome list was writen to GCF_000735715.2_ASM73571v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:07,309] [INFO] Task started: fastANI
[2024-01-25 18:16:07,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg96213e15-0670-4cca-8e7d-34821fcb6be2/GCF_000735715.2_ASM73571v2_genomic.fna.gz --refList GCF_000735715.2_ASM73571v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000735715.2_ASM73571v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:29,252] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:29,263] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:29,263] [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_000735715.2	s__Flavobacterium chungangense	100.0	1838	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	conclusive
GCF_003202405.1	s__Flavobacterium hydrophilum	87.4007	1270	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	85.4753	1199	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645075.1	s__Flavobacterium limi	85.1936	1259	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010645065.1	s__Flavobacterium fluviatile	84.8549	1062	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282055.1	s__Flavobacterium sp000282055	83.2902	1095	1844	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	82.472	1012	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003688345.1	s__Flavobacterium sp003688345	82.1836	1007	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001602525.1	s__Flavobacterium chilense	82.1127	936	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_000708595.2	s__Flavobacterium sp000708595	82.0856	912	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_900129795.1	s__Flavobacterium sp900129795	82.0583	981	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018383905.1	s__Flavobacterium branchiicola	82.0447	899	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	81.8297	928	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCA_002482975.1	s__Flavobacterium sp002482975	81.8159	961	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217395.1	s__Flavobacterium plurextorum	81.7837	837	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCA_900129595.1	s__Flavobacterium frigidimaris	81.768	945	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004368785.1	s__Flavobacterium sp004368785	81.6985	956	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182285.1	s__Flavobacterium sp015182285	81.2459	924	1844	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:29,265] [INFO] GTDB search result was written to GCF_000735715.2_ASM73571v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:29,266] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:29,269] [INFO] DFAST_QC result json was written to GCF_000735715.2_ASM73571v2_genomic.fna/dqc_result.json
[2024-01-25 18:16:29,270] [INFO] DFAST_QC completed!
[2024-01-25 18:16:29,270] [INFO] Total running time: 0h1m53s