[2024-01-24 11:59:13,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference
[2024-01-24 11:59:14,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,518] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgda1d11ec-7781-413a-a4b2-ca62a4b80049/GCF_017068455.1_ASM1706845v1_genomic.fna.gz | prodigal -d GCF_017068455.1_ASM1706845v1_genomic.fna/cds.fna -a GCF_017068455.1_ASM1706845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:30,605] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:30,606] [INFO] Task started: HMMsearch
[2024-01-24 11:59:30,606] [INFO] Running command: hmmsearch --tblout GCF_017068455.1_ASM1706845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/reference_markers.hmm GCF_017068455.1_ASM1706845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,994] [INFO] Found 6/6 markers.
[2024-01-24 11:59:31,032] [INFO] Query marker FASTA was written to GCF_017068455.1_ASM1706845v1_genomic.fna/markers.fasta
[2024-01-24 11:59:31,033] [INFO] Task started: Blastn
[2024-01-24 11:59:31,033] [INFO] Running command: blastn -query GCF_017068455.1_ASM1706845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/reference_markers.fasta -out GCF_017068455.1_ASM1706845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:31,689] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:31,692] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:31,693] [INFO] Target genome list was writen to GCF_017068455.1_ASM1706845v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:31,700] [INFO] Task started: fastANI
[2024-01-24 11:59:31,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1d11ec-7781-413a-a4b2-ca62a4b80049/GCF_017068455.1_ASM1706845v1_genomic.fna.gz --refList GCF_017068455.1_ASM1706845v1_genomic.fna/target_genomes.txt --output GCF_017068455.1_ASM1706845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:46,861] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:46,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:46,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:46,890] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:46,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:46,890] [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
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	100.0	1378	1379	95	conclusive
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	77.4057	178	1379	95	below_threshold
Marivirga tractuosa	strain=DSM 4126	GCA_000183425.1	1006	1006	type	True	76.8404	63	1379	95	below_threshold
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	76.5831	88	1379	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.4304	71	1379	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.3914	83	1379	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.3537	66	1379	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	76.1803	50	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:46,919] [INFO] DFAST Taxonomy check result was written to GCF_017068455.1_ASM1706845v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:46,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:46,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:46,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/checkm_data
[2024-01-24 11:59:46,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:46,967] [INFO] Task started: CheckM
[2024-01-24 11:59:46,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017068455.1_ASM1706845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017068455.1_ASM1706845v1_genomic.fna/checkm_input GCF_017068455.1_ASM1706845v1_genomic.fna/checkm_result
[2024-01-24 12:00:35,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:35,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:35,576] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:35,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:35,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017068455.1_ASM1706845v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:35,577] [INFO] Task started: Blastn
[2024-01-24 12:00:35,577] [INFO] Running command: blastn -query GCF_017068455.1_ASM1706845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf377fbd5-65dd-4e3c-98fa-903e560bfa0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017068455.1_ASM1706845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:36,458] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:36,463] [INFO] Selected 24 target genomes.
[2024-01-24 12:00:36,463] [INFO] Target genome list was writen to GCF_017068455.1_ASM1706845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:36,482] [INFO] Task started: fastANI
[2024-01-24 12:00:36,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1d11ec-7781-413a-a4b2-ca62a4b80049/GCF_017068455.1_ASM1706845v1_genomic.fna.gz --refList GCF_017068455.1_ASM1706845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017068455.1_ASM1706845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:52,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:52,511] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:52,511] [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_017068455.1	s__Fulvivirga sp017068455	100.0	1379	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009711525.1	s__Fulvivirga lutimaris	77.3739	180	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338655.1	s__Fulvivirga sp002338655	76.9693	132	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183425.1	s__Marivirga tractuosa	76.8404	63	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757215.1	s__Fulvivirga sp016757215	76.5831	88	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711405.1	s__Fulvivirga kasyanovii	76.4304	71	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.3914	83	1379	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:52,513] [INFO] GTDB search result was written to GCF_017068455.1_ASM1706845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:52,514] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:52,516] [INFO] DFAST_QC result json was written to GCF_017068455.1_ASM1706845v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:52,517] [INFO] DFAST_QC completed!
[2024-01-24 12:00:52,517] [INFO] Total running time: 0h1m39s