[2024-01-24 13:45:46,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference
[2024-01-24 13:45:47,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,824] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd448f22-7fca-43ee-a4b3-7bcf1d01d42d/GCF_014596935.1_ASM1459693v1_genomic.fna.gz | prodigal -d GCF_014596935.1_ASM1459693v1_genomic.fna/cds.fna -a GCF_014596935.1_ASM1459693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:01,438] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:01,438] [INFO] Task started: HMMsearch
[2024-01-24 13:46:01,438] [INFO] Running command: hmmsearch --tblout GCF_014596935.1_ASM1459693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/reference_markers.hmm GCF_014596935.1_ASM1459693v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:01,832] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:01,833] [INFO] Found 6/6 markers.
[2024-01-24 13:46:01,867] [INFO] Query marker FASTA was written to GCF_014596935.1_ASM1459693v1_genomic.fna/markers.fasta
[2024-01-24 13:46:01,867] [INFO] Task started: Blastn
[2024-01-24 13:46:01,867] [INFO] Running command: blastn -query GCF_014596935.1_ASM1459693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/reference_markers.fasta -out GCF_014596935.1_ASM1459693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:02,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:02,611] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:02,611] [INFO] Target genome list was writen to GCF_014596935.1_ASM1459693v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:02,626] [INFO] Task started: fastANI
[2024-01-24 13:46:02,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd448f22-7fca-43ee-a4b3-7bcf1d01d42d/GCF_014596935.1_ASM1459693v1_genomic.fna.gz --refList GCF_014596935.1_ASM1459693v1_genomic.fna/target_genomes.txt --output GCF_014596935.1_ASM1459693v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:14,778] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:14,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:14,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:14,791] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:14,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:14,791] [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
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	100.0	1332	1332	95	conclusive
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	84.8493	904	1332	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	81.0094	687	1332	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.4611	407	1332	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.3726	340	1332	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.3138	392	1332	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.1086	309	1332	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.9632	326	1332	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.9282	267	1332	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.8958	304	1332	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8102	302	1332	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.7913	293	1332	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.3604	248	1332	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.3172	245	1332	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.1539	164	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:14,794] [INFO] DFAST Taxonomy check result was written to GCF_014596935.1_ASM1459693v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:14,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:14,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:14,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/checkm_data
[2024-01-24 13:46:14,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:14,836] [INFO] Task started: CheckM
[2024-01-24 13:46:14,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596935.1_ASM1459693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596935.1_ASM1459693v1_genomic.fna/checkm_input GCF_014596935.1_ASM1459693v1_genomic.fna/checkm_result
[2024-01-24 13:46:57,772] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:57,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,795] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:57,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:57,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596935.1_ASM1459693v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:57,797] [INFO] Task started: Blastn
[2024-01-24 13:46:57,797] [INFO] Running command: blastn -query GCF_014596935.1_ASM1459693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg919d3e3b-0a0d-4a15-b970-bfc622bd5065/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596935.1_ASM1459693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,783] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,787] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:58,787] [INFO] Target genome list was writen to GCF_014596935.1_ASM1459693v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:58,796] [INFO] Task started: fastANI
[2024-01-24 13:46:58,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd448f22-7fca-43ee-a4b3-7bcf1d01d42d/GCF_014596935.1_ASM1459693v1_genomic.fna.gz --refList GCF_014596935.1_ASM1459693v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596935.1_ASM1459693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:06,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:06,767] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:06,767] [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_014596935.1	s__Aestuariibaculum suncheonense	100.0	1332	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014596975.1	s__Aestuariibaculum marinum	84.8582	903	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596945.1	s__Aestuariibaculum sediminum	81.0001	688	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	79.1174	401	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.6949	421	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.4474	409	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.3328	390	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.1001	311	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	78.0098	366	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.2312	217	1332	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,769] [INFO] GTDB search result was written to GCF_014596935.1_ASM1459693v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:06,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:06,773] [INFO] DFAST_QC result json was written to GCF_014596935.1_ASM1459693v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:06,773] [INFO] DFAST_QC completed!
[2024-01-24 13:47:06,773] [INFO] Total running time: 0h1m20s