[2024-01-24 13:48:43,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference
[2024-01-24 13:48:44,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,651] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg508fb360-7408-4fb6-a4c8-d9082c7e7730/GCF_004362665.1_ASM436266v1_genomic.fna.gz | prodigal -d GCF_004362665.1_ASM436266v1_genomic.fna/cds.fna -a GCF_004362665.1_ASM436266v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:56,214] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:56,214] [INFO] Task started: HMMsearch
[2024-01-24 13:48:56,214] [INFO] Running command: hmmsearch --tblout GCF_004362665.1_ASM436266v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/reference_markers.hmm GCF_004362665.1_ASM436266v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:56,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:56,450] [INFO] Found 6/6 markers.
[2024-01-24 13:48:56,481] [INFO] Query marker FASTA was written to GCF_004362665.1_ASM436266v1_genomic.fna/markers.fasta
[2024-01-24 13:48:56,481] [INFO] Task started: Blastn
[2024-01-24 13:48:56,481] [INFO] Running command: blastn -query GCF_004362665.1_ASM436266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/reference_markers.fasta -out GCF_004362665.1_ASM436266v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:57,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:57,176] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:57,176] [INFO] Target genome list was writen to GCF_004362665.1_ASM436266v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:57,193] [INFO] Task started: fastANI
[2024-01-24 13:48:57,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg508fb360-7408-4fb6-a4c8-d9082c7e7730/GCF_004362665.1_ASM436266v1_genomic.fna.gz --refList GCF_004362665.1_ASM436266v1_genomic.fna/target_genomes.txt --output GCF_004362665.1_ASM436266v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:06,077] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:06,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:06,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:06,090] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:06,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:06,090] [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 dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	100.0	1061	1061	95	conclusive
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	87.2958	700	1061	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	87.2389	693	1061	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	84.7183	665	1061	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	80.6282	495	1061	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	80.5783	491	1061	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	80.5352	500	1061	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	79.4605	463	1061	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	79.1733	454	1061	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.2625	292	1061	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.0701	298	1061	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.5377	247	1061	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.4723	185	1061	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.2767	245	1061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:06,105] [INFO] DFAST Taxonomy check result was written to GCF_004362665.1_ASM436266v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:06,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:06,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:06,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/checkm_data
[2024-01-24 13:49:06,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:06,145] [INFO] Task started: CheckM
[2024-01-24 13:49:06,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362665.1_ASM436266v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362665.1_ASM436266v1_genomic.fna/checkm_input GCF_004362665.1_ASM436266v1_genomic.fna/checkm_result
[2024-01-24 13:49:43,823] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:43,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:43,847] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:43,848] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:43,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362665.1_ASM436266v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:43,848] [INFO] Task started: Blastn
[2024-01-24 13:49:43,848] [INFO] Running command: blastn -query GCF_004362665.1_ASM436266v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea514e0b-5d7d-42ad-9c2e-efcb7e94c2ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362665.1_ASM436266v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,879] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,883] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:44,883] [INFO] Target genome list was writen to GCF_004362665.1_ASM436266v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:44,900] [INFO] Task started: fastANI
[2024-01-24 13:49:44,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg508fb360-7408-4fb6-a4c8-d9082c7e7730/GCF_004362665.1_ASM436266v1_genomic.fna.gz --refList GCF_004362665.1_ASM436266v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362665.1_ASM436266v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:53,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,262] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:53,262] [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_004362665.1	s__Flavobacterium dankookense	100.0	1061	1061	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_014486675.1	s__Flavobacterium macrobrachii	87.2389	693	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCF_012911605.1	s__Flavobacterium sp012911605	84.7066	666	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	80.5732	449	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	80.5084	503	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCA_001464475.1	s__Flavobacterium sp001464475	80.4587	498	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	80.0266	430	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642275.1	s__Flavobacterium lutivivi	79.4608	463	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	79.3436	479	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_004797125.1	s__Flavobacterium sangjuense	79.1733	454	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486695.1	s__Flavobacterium buctense	78.9579	443	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	78.1917	316	1061	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296885.1	s__Flavobacterium sp002296885	77.9629	258	1061	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 13:49:53,264] [INFO] GTDB search result was written to GCF_004362665.1_ASM436266v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:53,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:53,271] [INFO] DFAST_QC result json was written to GCF_004362665.1_ASM436266v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:53,271] [INFO] DFAST_QC completed!
[2024-01-24 13:49:53,271] [INFO] Total running time: 0h1m10s