[2024-01-24 12:29:26,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:26,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:26,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference
[2024-01-24 12:29:28,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,284] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f916061-c964-4a4f-9e5a-c213d046c9f3/GCF_003385115.1_ASM338511v1_genomic.fna.gz | prodigal -d GCF_003385115.1_ASM338511v1_genomic.fna/cds.fna -a GCF_003385115.1_ASM338511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:46,625] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:46,626] [INFO] Task started: HMMsearch
[2024-01-24 12:29:46,626] [INFO] Running command: hmmsearch --tblout GCF_003385115.1_ASM338511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/reference_markers.hmm GCF_003385115.1_ASM338511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:47,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:47,024] [INFO] Found 6/6 markers.
[2024-01-24 12:29:47,067] [INFO] Query marker FASTA was written to GCF_003385115.1_ASM338511v1_genomic.fna/markers.fasta
[2024-01-24 12:29:47,068] [INFO] Task started: Blastn
[2024-01-24 12:29:47,068] [INFO] Running command: blastn -query GCF_003385115.1_ASM338511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/reference_markers.fasta -out GCF_003385115.1_ASM338511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:47,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:47,825] [INFO] Selected 17 target genomes.
[2024-01-24 12:29:47,826] [INFO] Target genome list was writen to GCF_003385115.1_ASM338511v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:47,842] [INFO] Task started: fastANI
[2024-01-24 12:29:47,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f916061-c964-4a4f-9e5a-c213d046c9f3/GCF_003385115.1_ASM338511v1_genomic.fna.gz --refList GCF_003385115.1_ASM338511v1_genomic.fna/target_genomes.txt --output GCF_003385115.1_ASM338511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:04,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:04,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:04,669] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:04,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:04,669] [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 aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	100.0	1679	1683	95	conclusive
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	81.7879	822	1683	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	81.4965	836	1683	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	80.7832	655	1683	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	80.7106	687	1683	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	80.3437	676	1683	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	79.1737	420	1683	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.0714	422	1683	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	78.9264	521	1683	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.715	455	1683	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.6907	530	1683	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	78.6105	500	1683	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	78.5873	545	1683	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	78.5853	514	1683	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4926	484	1683	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.4262	491	1683	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.807	134	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,671] [INFO] DFAST Taxonomy check result was written to GCF_003385115.1_ASM338511v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:04,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:04,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:04,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/checkm_data
[2024-01-24 12:30:04,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:04,735] [INFO] Task started: CheckM
[2024-01-24 12:30:04,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385115.1_ASM338511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385115.1_ASM338511v1_genomic.fna/checkm_input GCF_003385115.1_ASM338511v1_genomic.fna/checkm_result
[2024-01-24 12:31:01,884] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:01,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:01,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:01,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:01,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385115.1_ASM338511v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:01,917] [INFO] Task started: Blastn
[2024-01-24 12:31:01,917] [INFO] Running command: blastn -query GCF_003385115.1_ASM338511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23944774-0cb5-4b3a-a76c-6e54a4dbd0e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385115.1_ASM338511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:02,885] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:02,890] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:02,891] [INFO] Target genome list was writen to GCF_003385115.1_ASM338511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:02,908] [INFO] Task started: fastANI
[2024-01-24 12:31:02,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f916061-c964-4a4f-9e5a-c213d046c9f3/GCF_003385115.1_ASM338511v1_genomic.fna.gz --refList GCF_003385115.1_ASM338511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385115.1_ASM338511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:11,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,903] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:11,904] [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_003385115.1	s__Flavobacterium aquicola	100.0	1679	1683	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_015351475.1	s__Flavobacterium sp015351475	85.9412	1050	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	84.036	1018	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	82.7095	1028	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	82.1904	816	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	81.8354	843	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_001761465.1	s__Flavobacterium gilvum	80.7093	686	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009909155.2	s__Flavobacterium undicola	79.0627	423	1683	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 12:31:11,905] [INFO] GTDB search result was written to GCF_003385115.1_ASM338511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:11,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:11,910] [INFO] DFAST_QC result json was written to GCF_003385115.1_ASM338511v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:11,911] [INFO] DFAST_QC completed!
[2024-01-24 12:31:11,911] [INFO] Total running time: 0h1m45s