[2024-01-24 12:21:36,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference
[2024-01-24 12:21:37,428] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,429] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,429] [INFO] Running command: gunzip -c /var/lib/cwl/stg408a0f3e-d959-4ce0-ba3e-988041bb32e2/GCF_003254095.1_ASM325409v1_genomic.fna.gz | prodigal -d GCF_003254095.1_ASM325409v1_genomic.fna/cds.fna -a GCF_003254095.1_ASM325409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:49,766] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:49,767] [INFO] Task started: HMMsearch
[2024-01-24 12:21:49,767] [INFO] Running command: hmmsearch --tblout GCF_003254095.1_ASM325409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/reference_markers.hmm GCF_003254095.1_ASM325409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:50,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:50,036] [INFO] Found 6/6 markers.
[2024-01-24 12:21:50,066] [INFO] Query marker FASTA was written to GCF_003254095.1_ASM325409v1_genomic.fna/markers.fasta
[2024-01-24 12:21:50,067] [INFO] Task started: Blastn
[2024-01-24 12:21:50,067] [INFO] Running command: blastn -query GCF_003254095.1_ASM325409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/reference_markers.fasta -out GCF_003254095.1_ASM325409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:50,739] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:50,744] [INFO] Selected 10 target genomes.
[2024-01-24 12:21:50,744] [INFO] Target genome list was writen to GCF_003254095.1_ASM325409v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:50,752] [INFO] Task started: fastANI
[2024-01-24 12:21:50,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg408a0f3e-d959-4ce0-ba3e-988041bb32e2/GCF_003254095.1_ASM325409v1_genomic.fna.gz --refList GCF_003254095.1_ASM325409v1_genomic.fna/target_genomes.txt --output GCF_003254095.1_ASM325409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:58,710] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:58,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:58,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:58,723] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:21:58,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:58,723] [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
Salegentibacter mishustinae	strain=DSM 23404	GCA_003254095.1	270918	270918	type	True	99.9998	1243	1244	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	99.9874	1243	1244	95	conclusive
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	99.9841	1230	1244	95	conclusive
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	99.9837	1235	1244	95	conclusive
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	92.4471	947	1244	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	84.2523	867	1244	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	83.1646	837	1244	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2784	65	1244	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1632	89	1244	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0155	94	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:58,730] [INFO] DFAST Taxonomy check result was written to GCF_003254095.1_ASM325409v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:58,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:58,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:58,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/checkm_data
[2024-01-24 12:21:58,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:58,778] [INFO] Task started: CheckM
[2024-01-24 12:21:58,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254095.1_ASM325409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254095.1_ASM325409v1_genomic.fna/checkm_input GCF_003254095.1_ASM325409v1_genomic.fna/checkm_result
[2024-01-24 12:22:37,198] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:37,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,245] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:37,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:37,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254095.1_ASM325409v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:37,246] [INFO] Task started: Blastn
[2024-01-24 12:22:37,246] [INFO] Running command: blastn -query GCF_003254095.1_ASM325409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6179c2ec-54ec-4bc1-a9b5-98a9c35499e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254095.1_ASM325409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:38,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:38,232] [INFO] Selected 7 target genomes.
[2024-01-24 12:22:38,233] [INFO] Target genome list was writen to GCF_003254095.1_ASM325409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:38,239] [INFO] Task started: fastANI
[2024-01-24 12:22:38,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg408a0f3e-d959-4ce0-ba3e-988041bb32e2/GCF_003254095.1_ASM325409v1_genomic.fna.gz --refList GCF_003254095.1_ASM325409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254095.1_ASM325409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:44,797] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:44,809] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:44,809] [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_002900095.1	s__Salegentibacter mishustinae	99.9874	1243	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_900168265.1	s__Salegentibacter salarius	92.4693	961	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168045.1	s__Salegentibacter holothuriorum	86.9224	915	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.6974	926	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	85.6472	911	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900142975.1	s__Salegentibacter salegens	85.0341	909	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168115.1	s__Salegentibacter salinarum	83.1776	826	1244	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:44,811] [INFO] GTDB search result was written to GCF_003254095.1_ASM325409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:44,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:44,815] [INFO] DFAST_QC result json was written to GCF_003254095.1_ASM325409v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:44,815] [INFO] DFAST_QC completed!
[2024-01-24 12:22:44,815] [INFO] Total running time: 0h1m9s