[2024-01-24 14:39:45,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg69b0732d-8114-4820-80ef-2094eea30c8d/GCF_002833365.1_ASM283336v1_genomic.fna.gz | prodigal -d GCF_002833365.1_ASM283336v1_genomic.fna/cds.fna -a GCF_002833365.1_ASM283336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:02,502] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:02,503] [INFO] Task started: HMMsearch
[2024-01-24 14:40:02,503] [INFO] Running command: hmmsearch --tblout GCF_002833365.1_ASM283336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/reference_markers.hmm GCF_002833365.1_ASM283336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:02,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:02,805] [INFO] Found 6/6 markers.
[2024-01-24 14:40:02,846] [INFO] Query marker FASTA was written to GCF_002833365.1_ASM283336v1_genomic.fna/markers.fasta
[2024-01-24 14:40:02,846] [INFO] Task started: Blastn
[2024-01-24 14:40:02,847] [INFO] Running command: blastn -query GCF_002833365.1_ASM283336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/reference_markers.fasta -out GCF_002833365.1_ASM283336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:03,529] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:03,532] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:03,533] [INFO] Target genome list was writen to GCF_002833365.1_ASM283336v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:03,540] [INFO] Task started: fastANI
[2024-01-24 14:40:03,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b0732d-8114-4820-80ef-2094eea30c8d/GCF_002833365.1_ASM283336v1_genomic.fna.gz --refList GCF_002833365.1_ASM283336v1_genomic.fna/target_genomes.txt --output GCF_002833365.1_ASM283336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,015] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,031] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:13,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,032] [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 salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	100.0	1406	1411	95	conclusive
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	99.9973	1406	1411	95	conclusive
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	88.5082	1024	1411	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	86.9552	986	1411	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	86.917	1009	1411	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	86.59	973	1411	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	84.6991	896	1411	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6127	79	1411	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.4366	60	1411	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1593	100	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,034] [INFO] DFAST Taxonomy check result was written to GCF_002833365.1_ASM283336v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/checkm_data
[2024-01-24 14:40:13,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,079] [INFO] Task started: CheckM
[2024-01-24 14:40:13,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002833365.1_ASM283336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002833365.1_ASM283336v1_genomic.fna/checkm_input GCF_002833365.1_ASM283336v1_genomic.fna/checkm_result
[2024-01-24 14:40:56,880] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:56,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:56,904] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:56,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:56,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002833365.1_ASM283336v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:56,905] [INFO] Task started: Blastn
[2024-01-24 14:40:56,905] [INFO] Running command: blastn -query GCF_002833365.1_ASM283336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d9570d-1598-4b22-8887-1e56fd20f5a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002833365.1_ASM283336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:57,802] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:57,806] [INFO] Selected 7 target genomes.
[2024-01-24 14:40:57,806] [INFO] Target genome list was writen to GCF_002833365.1_ASM283336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:57,812] [INFO] Task started: fastANI
[2024-01-24 14:40:57,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b0732d-8114-4820-80ef-2094eea30c8d/GCF_002833365.1_ASM283336v1_genomic.fna.gz --refList GCF_002833365.1_ASM283336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002833365.1_ASM283336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:04,398] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:04,405] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:04,406] [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_900168115.1	s__Salegentibacter salinarum	99.9973	1406	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900113135.1	s__Salegentibacter agarivorans	88.4724	1027	1411	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	86.951	1005	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168265.1	s__Salegentibacter salarius	83.4329	818	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_000745315.1	s__Salegentibacter sp000745315	83.3222	889	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900095.1	s__Salegentibacter mishustinae	83.0486	849	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900168045.1	s__Salegentibacter holothuriorum	82.3913	794	1411	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:04,407] [INFO] GTDB search result was written to GCF_002833365.1_ASM283336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:04,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:04,411] [INFO] DFAST_QC result json was written to GCF_002833365.1_ASM283336v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:04,412] [INFO] DFAST_QC completed!
[2024-01-24 14:41:04,412] [INFO] Total running time: 0h1m19s