[2024-01-24 12:46:57,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference
[2024-01-24 12:46:59,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:59,192] [INFO] Task started: Prodigal
[2024-01-24 12:46:59,193] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dffca4a-900e-48ee-a32b-002889ae2c5c/GCF_006539785.1_ASM653978v1_genomic.fna.gz | prodigal -d GCF_006539785.1_ASM653978v1_genomic.fna/cds.fna -a GCF_006539785.1_ASM653978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:11,137] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:11,137] [INFO] Task started: HMMsearch
[2024-01-24 12:47:11,137] [INFO] Running command: hmmsearch --tblout GCF_006539785.1_ASM653978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/reference_markers.hmm GCF_006539785.1_ASM653978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:11,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:11,394] [INFO] Found 6/6 markers.
[2024-01-24 12:47:11,427] [INFO] Query marker FASTA was written to GCF_006539785.1_ASM653978v1_genomic.fna/markers.fasta
[2024-01-24 12:47:11,427] [INFO] Task started: Blastn
[2024-01-24 12:47:11,427] [INFO] Running command: blastn -query GCF_006539785.1_ASM653978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/reference_markers.fasta -out GCF_006539785.1_ASM653978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:12,119] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:12,122] [INFO] Selected 16 target genomes.
[2024-01-24 12:47:12,122] [INFO] Target genome list was writen to GCF_006539785.1_ASM653978v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:12,128] [INFO] Task started: fastANI
[2024-01-24 12:47:12,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dffca4a-900e-48ee-a32b-002889ae2c5c/GCF_006539785.1_ASM653978v1_genomic.fna.gz --refList GCF_006539785.1_ASM653978v1_genomic.fna/target_genomes.txt --output GCF_006539785.1_ASM653978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:23,653] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:23,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:23,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:23,668] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:47:23,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:23,668] [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 aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	100.0	1131	1133	95	conclusive
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	99.9984	1133	1133	95	conclusive
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	99.9939	1131	1133	95	conclusive
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	80.6482	484	1133	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	80.2306	486	1133	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	80.2187	480	1133	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	79.9486	471	1133	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.4441	335	1133	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	78.3893	386	1133	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.794	276	1133	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	77.706	306	1133	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.6112	286	1133	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	77.5791	288	1133	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.5309	296	1133	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.1381	169	1133	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.0817	176	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:23,671] [INFO] DFAST Taxonomy check result was written to GCF_006539785.1_ASM653978v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:23,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:23,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:23,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/checkm_data
[2024-01-24 12:47:23,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:23,710] [INFO] Task started: CheckM
[2024-01-24 12:47:23,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539785.1_ASM653978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539785.1_ASM653978v1_genomic.fna/checkm_input GCF_006539785.1_ASM653978v1_genomic.fna/checkm_result
[2024-01-24 12:48:02,208] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:02,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,225] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:02,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:02,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539785.1_ASM653978v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:02,226] [INFO] Task started: Blastn
[2024-01-24 12:48:02,226] [INFO] Running command: blastn -query GCF_006539785.1_ASM653978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc785d264-51c9-4cf3-bf2f-7d711aa64d3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539785.1_ASM653978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:03,259] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:03,263] [INFO] Selected 8 target genomes.
[2024-01-24 12:48:03,264] [INFO] Target genome list was writen to GCF_006539785.1_ASM653978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:03,271] [INFO] Task started: fastANI
[2024-01-24 12:48:03,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dffca4a-900e-48ee-a32b-002889ae2c5c/GCF_006539785.1_ASM653978v1_genomic.fna.gz --refList GCF_006539785.1_ASM653978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539785.1_ASM653978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:08,788] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:08,799] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:08,799] [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_000757385.1	s__Flavobacterium aquatile	99.9984	1133	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCA_003525665.1	s__Flavobacterium sp003525665	89.6917	766	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	82.7725	659	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	82.2088	554	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	80.6861	481	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913315.1	s__Flavobacterium sp903913315	80.0247	403	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903838055.1	s__Flavobacterium sp903838055	79.653	391	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
GCA_903888655.1	s__Flavobacterium sp903888655	79.3717	298	1133	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 12:48:08,801] [INFO] GTDB search result was written to GCF_006539785.1_ASM653978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:08,802] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:08,808] [INFO] DFAST_QC result json was written to GCF_006539785.1_ASM653978v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:08,808] [INFO] DFAST_QC completed!
[2024-01-24 12:48:08,808] [INFO] Total running time: 0h1m11s