[2024-01-24 13:40:34,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference
[2024-01-24 13:40:36,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,364] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aed1b5a-bc3e-4926-82d7-c7bcb2e5f496/GCF_006491645.1_ASM649164v1_genomic.fna.gz | prodigal -d GCF_006491645.1_ASM649164v1_genomic.fna/cds.fna -a GCF_006491645.1_ASM649164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,270] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,270] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,270] [INFO] Running command: hmmsearch --tblout GCF_006491645.1_ASM649164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/reference_markers.hmm GCF_006491645.1_ASM649164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,602] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,639] [INFO] Query marker FASTA was written to GCF_006491645.1_ASM649164v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,639] [INFO] Task started: Blastn
[2024-01-24 13:40:49,640] [INFO] Running command: blastn -query GCF_006491645.1_ASM649164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/reference_markers.fasta -out GCF_006491645.1_ASM649164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,369] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:50,369] [INFO] Target genome list was writen to GCF_006491645.1_ASM649164v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,373] [INFO] Task started: fastANI
[2024-01-24 13:40:50,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aed1b5a-bc3e-4926-82d7-c7bcb2e5f496/GCF_006491645.1_ASM649164v1_genomic.fna.gz --refList GCF_006491645.1_ASM649164v1_genomic.fna/target_genomes.txt --output GCF_006491645.1_ASM649164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,763] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,778] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:58,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:58,779] [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 profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	100.0	1321	1321	95	conclusive
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	100.0	1321	1321	95	conclusive
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	81.2466	824	1321	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	79.4915	575	1321	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.9431	572	1321	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.5634	369	1321	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.5411	345	1321	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.4974	372	1321	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.4028	357	1321	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	77.7752	290	1321	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.6491	145	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,781] [INFO] DFAST Taxonomy check result was written to GCF_006491645.1_ASM649164v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,782] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/checkm_data
[2024-01-24 13:40:58,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,834] [INFO] Task started: CheckM
[2024-01-24 13:40:58,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006491645.1_ASM649164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006491645.1_ASM649164v1_genomic.fna/checkm_input GCF_006491645.1_ASM649164v1_genomic.fna/checkm_result
[2024-01-24 13:41:42,619] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:42,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,647] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:42,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:42,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006491645.1_ASM649164v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:42,648] [INFO] Task started: Blastn
[2024-01-24 13:41:42,648] [INFO] Running command: blastn -query GCF_006491645.1_ASM649164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94375876-fc0f-4ced-a651-b334711a6091/dqc_reference/reference_markers_gtdb.fasta -out GCF_006491645.1_ASM649164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:43,649] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:43,653] [INFO] Selected 6 target genomes.
[2024-01-24 13:41:43,653] [INFO] Target genome list was writen to GCF_006491645.1_ASM649164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:43,658] [INFO] Task started: fastANI
[2024-01-24 13:41:43,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aed1b5a-bc3e-4926-82d7-c7bcb2e5f496/GCF_006491645.1_ASM649164v1_genomic.fna.gz --refList GCF_006491645.1_ASM649164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006491645.1_ASM649164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:50,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,596] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:50,596] [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_006491645.1	s__Flavobacterium sp006491645	100.0	1321	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002862755.1	s__Flavobacterium sp002862755	94.4521	1052	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	92.3383	1044	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	85.3107	893	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	84.7793	938	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	81.2493	823	1321	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 13:41:50,599] [INFO] GTDB search result was written to GCF_006491645.1_ASM649164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:50,599] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:50,603] [INFO] DFAST_QC result json was written to GCF_006491645.1_ASM649164v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:50,603] [INFO] DFAST_QC completed!
[2024-01-24 13:41:50,603] [INFO] Total running time: 0h1m16s