[2024-01-24 12:22:27,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:27,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:27,408] [INFO] DQC Reference Directory: /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference
[2024-01-24 12:22:28,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:28,822] [INFO] Task started: Prodigal
[2024-01-24 12:22:28,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg75bb6363-c5a9-4365-a27a-da7a41382147/GCF_000425465.1_ASM42546v1_genomic.fna.gz | prodigal -d GCF_000425465.1_ASM42546v1_genomic.fna/cds.fna -a GCF_000425465.1_ASM42546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:41,877] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:41,878] [INFO] Task started: HMMsearch
[2024-01-24 12:22:41,878] [INFO] Running command: hmmsearch --tblout GCF_000425465.1_ASM42546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/reference_markers.hmm GCF_000425465.1_ASM42546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:42,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:42,231] [INFO] Found 6/6 markers.
[2024-01-24 12:22:42,267] [INFO] Query marker FASTA was written to GCF_000425465.1_ASM42546v1_genomic.fna/markers.fasta
[2024-01-24 12:22:42,268] [INFO] Task started: Blastn
[2024-01-24 12:22:42,268] [INFO] Running command: blastn -query GCF_000425465.1_ASM42546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/reference_markers.fasta -out GCF_000425465.1_ASM42546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:43,065] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:43,068] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:43,069] [INFO] Target genome list was writen to GCF_000425465.1_ASM42546v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:43,075] [INFO] Task started: fastANI
[2024-01-24 12:22:43,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bb6363-c5a9-4365-a27a-da7a41382147/GCF_000425465.1_ASM42546v1_genomic.fna.gz --refList GCF_000425465.1_ASM42546v1_genomic.fna/target_genomes.txt --output GCF_000425465.1_ASM42546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:54,082] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:54,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:54,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:54,096] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:54,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:54,097] [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 filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	100.0	1034	1036	95	conclusive
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	83.2411	677	1036	95	below_threshold
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	81.7874	625	1036	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	80.692	479	1036	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.022	288	1036	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.9736	288	1036	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	77.8802	298	1036	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.6698	271	1036	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.5848	268	1036	95	below_threshold
Flavobacterium restrictum	strain=LB1R34	GCA_007097245.1	2594428	2594428	type	True	77.5094	160	1036	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.4409	146	1036	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	77.4209	214	1036	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.3985	192	1036	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.2992	152	1036	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.1634	199	1036	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.0999	142	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:54,099] [INFO] DFAST Taxonomy check result was written to GCF_000425465.1_ASM42546v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:54,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:54,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:54,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/checkm_data
[2024-01-24 12:22:54,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:54,137] [INFO] Task started: CheckM
[2024-01-24 12:22:54,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425465.1_ASM42546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425465.1_ASM42546v1_genomic.fna/checkm_input GCF_000425465.1_ASM42546v1_genomic.fna/checkm_result
[2024-01-24 12:23:35,150] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:35,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,176] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:35,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:35,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425465.1_ASM42546v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:35,177] [INFO] Task started: Blastn
[2024-01-24 12:23:35,177] [INFO] Running command: blastn -query GCF_000425465.1_ASM42546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9b70c96-dc5c-40df-9fad-71a6481ff4c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425465.1_ASM42546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:36,108] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:36,113] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:36,113] [INFO] Target genome list was writen to GCF_000425465.1_ASM42546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:36,128] [INFO] Task started: fastANI
[2024-01-24 12:23:36,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bb6363-c5a9-4365-a27a-da7a41382147/GCF_000425465.1_ASM42546v1_genomic.fna.gz --refList GCF_000425465.1_ASM42546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425465.1_ASM42546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:43,658] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:43,674] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:43,674] [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_000425465.1	s__Flavobacterium filum	100.0	1035	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017302935.1	s__Flavobacterium sp017302935	94.4708	748	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	83.2297	678	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCA_002352205.1	s__Flavobacterium sp002352205	82.1404	666	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCF_003268815.1	s__Flavobacterium lacus	81.7874	625	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428305.1	s__Flavobacterium sp002428305	80.7679	469	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	80.6916	479	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822155.1	s__Flavobacterium sp013822155	79.8956	529	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	77.8712	298	1036	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	77.6957	193	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCF_007097245.1	s__Flavobacterium sp007097245	77.5286	159	1036	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 12:23:43,676] [INFO] GTDB search result was written to GCF_000425465.1_ASM42546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:43,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:43,681] [INFO] DFAST_QC result json was written to GCF_000425465.1_ASM42546v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:43,681] [INFO] DFAST_QC completed!
[2024-01-24 12:23:43,681] [INFO] Total running time: 0h1m16s