[2024-01-24 13:18:32,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference
[2024-01-24 13:18:33,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,990] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,990] [INFO] Running command: gunzip -c /var/lib/cwl/stg159dfc41-03db-4fc8-9b08-68f2f7078c8c/GCF_014639535.1_ASM1463953v1_genomic.fna.gz | prodigal -d GCF_014639535.1_ASM1463953v1_genomic.fna/cds.fna -a GCF_014639535.1_ASM1463953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:49,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:49,590] [INFO] Task started: HMMsearch
[2024-01-24 13:18:49,590] [INFO] Running command: hmmsearch --tblout GCF_014639535.1_ASM1463953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/reference_markers.hmm GCF_014639535.1_ASM1463953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:49,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:49,970] [INFO] Found 6/6 markers.
[2024-01-24 13:18:50,003] [INFO] Query marker FASTA was written to GCF_014639535.1_ASM1463953v1_genomic.fna/markers.fasta
[2024-01-24 13:18:50,003] [INFO] Task started: Blastn
[2024-01-24 13:18:50,003] [INFO] Running command: blastn -query GCF_014639535.1_ASM1463953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/reference_markers.fasta -out GCF_014639535.1_ASM1463953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,734] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,738] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:50,738] [INFO] Target genome list was writen to GCF_014639535.1_ASM1463953v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:50,747] [INFO] Task started: fastANI
[2024-01-24 13:18:50,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg159dfc41-03db-4fc8-9b08-68f2f7078c8c/GCF_014639535.1_ASM1463953v1_genomic.fna.gz --refList GCF_014639535.1_ASM1463953v1_genomic.fna/target_genomes.txt --output GCF_014639535.1_ASM1463953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:05,550] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:05,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:05,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:05,575] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:05,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:05,575] [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 palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	100.0	1308	1308	95	conclusive
Flavobacterium glycines	strain=NBRC 105008	GCA_001686935.1	551990	551990	type	True	87.1477	966	1308	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	87.0704	969	1308	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	87.0455	964	1308	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	86.684	1056	1308	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	84.8604	972	1308	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	84.2953	899	1308	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	83.4798	857	1308	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	83.3744	884	1308	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	83.0933	883	1308	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	83.0864	882	1308	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.903	413	1308	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.8738	416	1308	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.8022	438	1308	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.6019	456	1308	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.2922	127	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:05,577] [INFO] DFAST Taxonomy check result was written to GCF_014639535.1_ASM1463953v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:05,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:05,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:05,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/checkm_data
[2024-01-24 13:19:05,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:05,619] [INFO] Task started: CheckM
[2024-01-24 13:19:05,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639535.1_ASM1463953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639535.1_ASM1463953v1_genomic.fna/checkm_input GCF_014639535.1_ASM1463953v1_genomic.fna/checkm_result
[2024-01-24 13:19:51,232] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:51,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,256] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:51,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:51,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639535.1_ASM1463953v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:51,257] [INFO] Task started: Blastn
[2024-01-24 13:19:51,257] [INFO] Running command: blastn -query GCF_014639535.1_ASM1463953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1465ac-5e64-452b-92ff-76216e5d7280/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639535.1_ASM1463953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:52,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:52,296] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:52,296] [INFO] Target genome list was writen to GCF_014639535.1_ASM1463953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:52,306] [INFO] Task started: fastANI
[2024-01-24 13:19:52,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg159dfc41-03db-4fc8-9b08-68f2f7078c8c/GCF_014639535.1_ASM1463953v1_genomic.fna.gz --refList GCF_014639535.1_ASM1463953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639535.1_ASM1463953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:01,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:01,684] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:01,684] [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_014639535.1	s__Flavobacterium palustre	100.0	1308	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100165.1	s__Flavobacterium glycines	87.0686	969	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001857965.1	s__Flavobacterium commune	86.6732	1058	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_004016525.1	s__Flavobacterium sufflavum	84.8608	972	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	84.2916	900	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	83.9033	702	1308	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	83.4869	856	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425425.1	s__Flavobacterium daejeonense	83.3665	885	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	83.1217	906	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014596575.1	s__Flavobacterium pokkalii	83.0868	882	1308	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.93	96.93	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:01,686] [INFO] GTDB search result was written to GCF_014639535.1_ASM1463953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:01,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:01,691] [INFO] DFAST_QC result json was written to GCF_014639535.1_ASM1463953v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:01,691] [INFO] DFAST_QC completed!
[2024-01-24 13:20:01,692] [INFO] Total running time: 0h1m29s