[2024-01-25 19:08:05,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:05,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:05,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference
[2024-01-25 19:08:06,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:06,668] [INFO] Task started: Prodigal
[2024-01-25 19:08:06,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e49a56c-8bd9-431a-92e2-b9439cf90de9/GCF_014596575.1_ASM1459657v1_genomic.fna.gz | prodigal -d GCF_014596575.1_ASM1459657v1_genomic.fna/cds.fna -a GCF_014596575.1_ASM1459657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:18,649] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:18,650] [INFO] Task started: HMMsearch
[2024-01-25 19:08:18,650] [INFO] Running command: hmmsearch --tblout GCF_014596575.1_ASM1459657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/reference_markers.hmm GCF_014596575.1_ASM1459657v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:18,911] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:18,912] [INFO] Found 6/6 markers.
[2024-01-25 19:08:18,943] [INFO] Query marker FASTA was written to GCF_014596575.1_ASM1459657v1_genomic.fna/markers.fasta
[2024-01-25 19:08:18,943] [INFO] Task started: Blastn
[2024-01-25 19:08:18,943] [INFO] Running command: blastn -query GCF_014596575.1_ASM1459657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/reference_markers.fasta -out GCF_014596575.1_ASM1459657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:19,611] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:19,613] [INFO] Selected 13 target genomes.
[2024-01-25 19:08:19,613] [INFO] Target genome list was writen to GCF_014596575.1_ASM1459657v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:19,628] [INFO] Task started: fastANI
[2024-01-25 19:08:19,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e49a56c-8bd9-431a-92e2-b9439cf90de9/GCF_014596575.1_ASM1459657v1_genomic.fna.gz --refList GCF_014596575.1_ASM1459657v1_genomic.fna/target_genomes.txt --output GCF_014596575.1_ASM1459657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:31,379] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:31,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:31,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:31,388] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:31,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:31,388] [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 pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	100.0	1265	1269	95	conclusive
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	94.1998	1054	1269	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	83.671	894	1269	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_001686935.1	551990	551990	type	True	83.6332	899	1269	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	83.5722	904	1269	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	83.1068	880	1269	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	82.2846	839	1269	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	82.0906	827	1269	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.5447	397	1269	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.4336	381	1269	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4176	415	1269	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.2962	419	1269	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.0353	134	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:31,390] [INFO] DFAST Taxonomy check result was written to GCF_014596575.1_ASM1459657v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:31,391] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:31,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:31,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/checkm_data
[2024-01-25 19:08:31,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:31,431] [INFO] Task started: CheckM
[2024-01-25 19:08:31,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596575.1_ASM1459657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596575.1_ASM1459657v1_genomic.fna/checkm_input GCF_014596575.1_ASM1459657v1_genomic.fna/checkm_result
[2024-01-25 19:09:08,277] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:08,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:08,296] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:08,296] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:08,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596575.1_ASM1459657v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:08,297] [INFO] Task started: Blastn
[2024-01-25 19:09:08,297] [INFO] Running command: blastn -query GCF_014596575.1_ASM1459657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg654ebe05-2e9a-4132-a7fa-04085e12919a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596575.1_ASM1459657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:09,295] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:09,298] [INFO] Selected 8 target genomes.
[2024-01-25 19:09:09,298] [INFO] Target genome list was writen to GCF_014596575.1_ASM1459657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:09,307] [INFO] Task started: fastANI
[2024-01-25 19:09:09,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e49a56c-8bd9-431a-92e2-b9439cf90de9/GCF_014596575.1_ASM1459657v1_genomic.fna.gz --refList GCF_014596575.1_ASM1459657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596575.1_ASM1459657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:16,284] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:16,290] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:16,290] [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_014596575.1	s__Flavobacterium pokkalii	100.0	1265	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.93	96.93	0.85	0.85	2	conclusive
GCF_000425425.1	s__Flavobacterium daejeonense	94.2186	1053	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100165.1	s__Flavobacterium glycines	83.6609	894	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014639535.1	s__Flavobacterium palustre	83.1143	880	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857965.1	s__Flavobacterium commune	82.2834	840	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCA_002454195.1	s__Flavobacterium sp002454195	82.2091	502	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	82.0906	827	1269	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	81.9326	756	1269	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 19:09:16,292] [INFO] GTDB search result was written to GCF_014596575.1_ASM1459657v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:16,292] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:16,295] [INFO] DFAST_QC result json was written to GCF_014596575.1_ASM1459657v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:16,295] [INFO] DFAST_QC completed!
[2024-01-25 19:09:16,295] [INFO] Total running time: 0h1m11s