[2024-01-24 13:49:26,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:26,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:26,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference
[2024-01-24 13:49:28,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,235] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,235] [INFO] Running command: gunzip -c /var/lib/cwl/stge80b20ae-25b5-4495-81f7-324ed1fc0386/GCF_000769895.1_ASM76989v1_genomic.fna.gz | prodigal -d GCF_000769895.1_ASM76989v1_genomic.fna/cds.fna -a GCF_000769895.1_ASM76989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:43,353] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:43,353] [INFO] Task started: HMMsearch
[2024-01-24 13:49:43,353] [INFO] Running command: hmmsearch --tblout GCF_000769895.1_ASM76989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/reference_markers.hmm GCF_000769895.1_ASM76989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,620] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,654] [INFO] Query marker FASTA was written to GCF_000769895.1_ASM76989v1_genomic.fna/markers.fasta
[2024-01-24 13:49:43,655] [INFO] Task started: Blastn
[2024-01-24 13:49:43,655] [INFO] Running command: blastn -query GCF_000769895.1_ASM76989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/reference_markers.fasta -out GCF_000769895.1_ASM76989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,429] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,432] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:44,432] [INFO] Target genome list was writen to GCF_000769895.1_ASM76989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:44,438] [INFO] Task started: fastANI
[2024-01-24 13:49:44,438] [INFO] Running command: fastANI --query /var/lib/cwl/stge80b20ae-25b5-4495-81f7-324ed1fc0386/GCF_000769895.1_ASM76989v1_genomic.fna.gz --refList GCF_000769895.1_ASM76989v1_genomic.fna/target_genomes.txt --output GCF_000769895.1_ASM76989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:54,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:54,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:54,135] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:54,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:54,135] [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 enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	100.0	1092	1094	95	conclusive
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	99.9913	1084	1094	95	conclusive
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	82.6524	747	1094	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	80.9133	587	1094	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	80.9006	589	1094	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	80.8051	605	1094	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	80.7343	625	1094	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	80.6572	609	1094	95	below_threshold
Flavobacterium suncheonense	strain=DSM 17707	GCA_000430025.1	350894	350894	type	True	79.3721	422	1094	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	79.2859	427	1094	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.9812	241	1094	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.8854	185	1094	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.8381	199	1094	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.8161	205	1094	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.5307	117	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,140] [INFO] DFAST Taxonomy check result was written to GCF_000769895.1_ASM76989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:54,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:54,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:54,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/checkm_data
[2024-01-24 13:49:54,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:54,192] [INFO] Task started: CheckM
[2024-01-24 13:49:54,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000769895.1_ASM76989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000769895.1_ASM76989v1_genomic.fna/checkm_input GCF_000769895.1_ASM76989v1_genomic.fna/checkm_result
[2024-01-24 13:50:38,026] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:38,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,048] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:38,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:38,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000769895.1_ASM76989v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:38,050] [INFO] Task started: Blastn
[2024-01-24 13:50:38,050] [INFO] Running command: blastn -query GCF_000769895.1_ASM76989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5875d6f5-ece2-40ef-9a45-bd0cb98f157f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000769895.1_ASM76989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,993] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:38,994] [INFO] Target genome list was writen to GCF_000769895.1_ASM76989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:39,004] [INFO] Task started: fastANI
[2024-01-24 13:50:39,005] [INFO] Running command: fastANI --query /var/lib/cwl/stge80b20ae-25b5-4495-81f7-324ed1fc0386/GCF_000769895.1_ASM76989v1_genomic.fna.gz --refList GCF_000769895.1_ASM76989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000769895.1_ASM76989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:44,129] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,143] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:44,143] [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_000498495.1	s__Flavobacterium enshiense	99.9913	1084	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000498535.1	s__Flavobacterium limnosediminis	82.6507	746	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100625.1	s__Flavobacterium saliperosum	80.8935	590	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000498475.1	s__Flavobacterium cauense	80.7219	625	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000430025.1	s__Flavobacterium suncheonense	79.3964	420	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013389455.1	s__Flavobacterium sp001898245	78.3655	309	1094	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	77.7149	123	1094	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 13:50:44,145] [INFO] GTDB search result was written to GCF_000769895.1_ASM76989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:44,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:44,151] [INFO] DFAST_QC result json was written to GCF_000769895.1_ASM76989v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:44,151] [INFO] DFAST_QC completed!
[2024-01-24 13:50:44,151] [INFO] Total running time: 0h1m17s