[2024-01-24 13:49:30,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference
[2024-01-24 13:49:32,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,095] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,095] [INFO] Running command: gunzip -c /var/lib/cwl/stga3fddb40-1879-4611-9874-d0b92444f3da/GCF_004016525.1_ASM401652v1_genomic.fna.gz | prodigal -d GCF_004016525.1_ASM401652v1_genomic.fna/cds.fna -a GCF_004016525.1_ASM401652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,985] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,985] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,985] [INFO] Running command: hmmsearch --tblout GCF_004016525.1_ASM401652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/reference_markers.hmm GCF_004016525.1_ASM401652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:48,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:48,340] [INFO] Found 6/6 markers.
[2024-01-24 13:49:48,379] [INFO] Query marker FASTA was written to GCF_004016525.1_ASM401652v1_genomic.fna/markers.fasta
[2024-01-24 13:49:48,379] [INFO] Task started: Blastn
[2024-01-24 13:49:48,379] [INFO] Running command: blastn -query GCF_004016525.1_ASM401652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/reference_markers.fasta -out GCF_004016525.1_ASM401652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:49,115] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:49,118] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:49,119] [INFO] Target genome list was writen to GCF_004016525.1_ASM401652v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:49,124] [INFO] Task started: fastANI
[2024-01-24 13:49:49,125] [INFO] Running command: fastANI --query /var/lib/cwl/stga3fddb40-1879-4611-9874-d0b92444f3da/GCF_004016525.1_ASM401652v1_genomic.fna.gz --refList GCF_004016525.1_ASM401652v1_genomic.fna/target_genomes.txt --output GCF_004016525.1_ASM401652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:03,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:03,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:03,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:03,079] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:03,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:03,079] [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 sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	100.0	1423	1425	95	conclusive
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	90.102	1088	1425	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	87.8709	966	1425	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	84.7279	975	1425	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	84.4003	969	1425	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	84.347	973	1425	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	83.983	849	1425	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	83.6222	861	1425	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	83.5631	892	1425	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.9805	440	1425	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.9389	439	1425	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.9192	471	1425	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.6619	437	1425	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.2755	124	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,081] [INFO] DFAST Taxonomy check result was written to GCF_004016525.1_ASM401652v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:03,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:03,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:03,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/checkm_data
[2024-01-24 13:50:03,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:03,130] [INFO] Task started: CheckM
[2024-01-24 13:50:03,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004016525.1_ASM401652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004016525.1_ASM401652v1_genomic.fna/checkm_input GCF_004016525.1_ASM401652v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,201] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,224] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,224] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004016525.1_ASM401652v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,225] [INFO] Task started: Blastn
[2024-01-24 13:50:51,225] [INFO] Running command: blastn -query GCF_004016525.1_ASM401652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f68b98-4966-4ea8-8cb2-84dd31a81c0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004016525.1_ASM401652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:52,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:52,169] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:52,169] [INFO] Target genome list was writen to GCF_004016525.1_ASM401652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:52,185] [INFO] Task started: fastANI
[2024-01-24 13:50:52,186] [INFO] Running command: fastANI --query /var/lib/cwl/stga3fddb40-1879-4611-9874-d0b92444f3da/GCF_004016525.1_ASM401652v1_genomic.fna.gz --refList GCF_004016525.1_ASM401652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004016525.1_ASM401652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:00,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:00,101] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:00,101] [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_004016525.1	s__Flavobacterium sufflavum	100.0	1423	1425	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_009909155.2	s__Flavobacterium undicola	90.0633	1092	1425	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	87.8571	967	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCA_002280815.1	s__Flavobacterium sp002280815	85.7	684	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639535.1	s__Flavobacterium palustre	84.7255	975	1425	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	84.3572	972	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000695795.1	s__Flavobacterium seoulense	83.9755	849	1425	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	83.5474	896	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:00,104] [INFO] GTDB search result was written to GCF_004016525.1_ASM401652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:00,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:00,109] [INFO] DFAST_QC result json was written to GCF_004016525.1_ASM401652v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:00,110] [INFO] DFAST_QC completed!
[2024-01-24 13:51:00,110] [INFO] Total running time: 0h1m29s