[2024-01-24 13:40:34,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference
[2024-01-24 13:40:36,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,131] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg47abc7b7-46cc-4145-8ea9-12fc34a3f173/GCF_010645075.1_ASM1064507v1_genomic.fna.gz | prodigal -d GCF_010645075.1_ASM1064507v1_genomic.fna/cds.fna -a GCF_010645075.1_ASM1064507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,805] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,806] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,806] [INFO] Running command: hmmsearch --tblout GCF_010645075.1_ASM1064507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/reference_markers.hmm GCF_010645075.1_ASM1064507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,178] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,225] [INFO] Query marker FASTA was written to GCF_010645075.1_ASM1064507v1_genomic.fna/markers.fasta
[2024-01-24 13:40:55,225] [INFO] Task started: Blastn
[2024-01-24 13:40:55,225] [INFO] Running command: blastn -query GCF_010645075.1_ASM1064507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/reference_markers.fasta -out GCF_010645075.1_ASM1064507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,965] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:55,965] [INFO] Target genome list was writen to GCF_010645075.1_ASM1064507v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,970] [INFO] Task started: fastANI
[2024-01-24 13:40:55,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg47abc7b7-46cc-4145-8ea9-12fc34a3f173/GCF_010645075.1_ASM1064507v1_genomic.fna.gz --refList GCF_010645075.1_ASM1064507v1_genomic.fna/target_genomes.txt --output GCF_010645075.1_ASM1064507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,072] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:13,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,072] [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 limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	100.0	1791	1793	95	conclusive
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	99.9836	1785	1793	95	conclusive
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	86.9534	1248	1793	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	86.7944	1370	1793	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	86.431	1162	1793	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	84.7315	1257	1793	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	81.8595	865	1793	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.8111	917	1793	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	81.7597	884	1793	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.554	878	1793	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.3942	924	1793	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.278	887	1793	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.1331	209	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,074] [INFO] DFAST Taxonomy check result was written to GCF_010645075.1_ASM1064507v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/checkm_data
[2024-01-24 13:41:13,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,127] [INFO] Task started: CheckM
[2024-01-24 13:41:13,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010645075.1_ASM1064507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010645075.1_ASM1064507v1_genomic.fna/checkm_input GCF_010645075.1_ASM1064507v1_genomic.fna/checkm_result
[2024-01-24 13:42:09,337] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:09,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:09,360] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:09,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:09,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010645075.1_ASM1064507v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:09,361] [INFO] Task started: Blastn
[2024-01-24 13:42:09,361] [INFO] Running command: blastn -query GCF_010645075.1_ASM1064507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7fcad2-5d94-4532-97ff-73ee3fd2f4f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_010645075.1_ASM1064507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,308] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:10,308] [INFO] Target genome list was writen to GCF_010645075.1_ASM1064507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,336] [INFO] Task started: fastANI
[2024-01-24 13:42:10,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg47abc7b7-46cc-4145-8ea9-12fc34a3f173/GCF_010645075.1_ASM1064507v1_genomic.fna.gz --refList GCF_010645075.1_ASM1064507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010645075.1_ASM1064507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:26,807] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:26,826] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:26,826] [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_010645075.1	s__Flavobacterium limi	100.0	1791	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003202405.1	s__Flavobacterium hydrophilum	86.7884	1371	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645065.1	s__Flavobacterium fluviatile	86.4413	1161	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	85.1338	1263	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010614725.1	s__Flavobacterium ajazii	84.7662	1221	1793	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	84.5366	1174	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	81.8854	861	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	81.8284	877	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017833855.1	s__Flavobacterium sp017833855	81.822	936	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	81.8188	903	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	81.6858	957	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142715.1	s__Flavobacterium pectinovorum	81.5688	992	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	81.5126	930	1793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000425445.1	s__Flavobacterium denitrificans	81.4294	880	1793	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 13:42:26,828] [INFO] GTDB search result was written to GCF_010645075.1_ASM1064507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:26,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:26,832] [INFO] DFAST_QC result json was written to GCF_010645075.1_ASM1064507v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:26,832] [INFO] DFAST_QC completed!
[2024-01-24 13:42:26,832] [INFO] Total running time: 0h1m52s