[2024-01-25 18:45:05,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference
[2024-01-25 18:45:06,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,685] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg788668fe-406b-4dd8-8238-0b66fed12ae7/GCF_016775155.1_ASM1677515v1_genomic.fna.gz | prodigal -d GCF_016775155.1_ASM1677515v1_genomic.fna/cds.fna -a GCF_016775155.1_ASM1677515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:31,437] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:31,437] [INFO] Task started: HMMsearch
[2024-01-25 18:45:31,437] [INFO] Running command: hmmsearch --tblout GCF_016775155.1_ASM1677515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/reference_markers.hmm GCF_016775155.1_ASM1677515v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:31,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:31,746] [INFO] Found 6/6 markers.
[2024-01-25 18:45:31,799] [INFO] Query marker FASTA was written to GCF_016775155.1_ASM1677515v1_genomic.fna/markers.fasta
[2024-01-25 18:45:31,800] [INFO] Task started: Blastn
[2024-01-25 18:45:31,800] [INFO] Running command: blastn -query GCF_016775155.1_ASM1677515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/reference_markers.fasta -out GCF_016775155.1_ASM1677515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:32,349] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:32,355] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:32,355] [INFO] Target genome list was writen to GCF_016775155.1_ASM1677515v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:32,366] [INFO] Task started: fastANI
[2024-01-25 18:45:32,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg788668fe-406b-4dd8-8238-0b66fed12ae7/GCF_016775155.1_ASM1677515v1_genomic.fna.gz --refList GCF_016775155.1_ASM1677515v1_genomic.fna/target_genomes.txt --output GCF_016775155.1_ASM1677515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:47,280] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:47,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:47,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:47,286] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:47,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:47,286] [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 marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	100.0	2231	2231	95	conclusive
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	80.2019	979	2231	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	77.6381	276	2231	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	76.948	94	2231	95	below_threshold
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	76.7167	146	2231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:47,288] [INFO] DFAST Taxonomy check result was written to GCF_016775155.1_ASM1677515v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:47,288] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:47,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:47,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/checkm_data
[2024-01-25 18:45:47,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:47,351] [INFO] Task started: CheckM
[2024-01-25 18:45:47,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016775155.1_ASM1677515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016775155.1_ASM1677515v1_genomic.fna/checkm_input GCF_016775155.1_ASM1677515v1_genomic.fna/checkm_result
[2024-01-25 18:47:03,494] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:03,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:03,518] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:03,518] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:03,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016775155.1_ASM1677515v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:03,520] [INFO] Task started: Blastn
[2024-01-25 18:47:03,520] [INFO] Running command: blastn -query GCF_016775155.1_ASM1677515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e117321-f1c9-4137-b8a9-f2fa33a7c716/dqc_reference/reference_markers_gtdb.fasta -out GCF_016775155.1_ASM1677515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:04,375] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:04,378] [INFO] Selected 22 target genomes.
[2024-01-25 18:47:04,378] [INFO] Target genome list was writen to GCF_016775155.1_ASM1677515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:04,396] [INFO] Task started: fastANI
[2024-01-25 18:47:04,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg788668fe-406b-4dd8-8238-0b66fed12ae7/GCF_016775155.1_ASM1677515v1_genomic.fna.gz --refList GCF_016775155.1_ASM1677515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016775155.1_ASM1677515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:25,620] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:25,626] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:25,626] [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_016775155.1	s__Fulvivirga sp016775155	100.0	2231	2231	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_009711405.1	s__Fulvivirga kasyanovii	80.1922	980	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	77.6495	275	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711525.1	s__Fulvivirga lutimaris	76.948	94	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757215.1	s__Fulvivirga sp016757215	76.7325	145	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657315.1	s__Fulvivirga sp001657315	76.3327	57	2231	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	76.2653	85	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012926615.1	s__Fabibacter_A sp012926615	75.8462	50	2231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:25,627] [INFO] GTDB search result was written to GCF_016775155.1_ASM1677515v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:25,628] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:25,630] [INFO] DFAST_QC result json was written to GCF_016775155.1_ASM1677515v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:25,630] [INFO] DFAST_QC completed!
[2024-01-25 18:47:25,630] [INFO] Total running time: 0h2m20s