[2024-01-24 12:36:34,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:34,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:34,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference
[2024-01-24 12:36:35,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:35,510] [INFO] Task started: Prodigal
[2024-01-24 12:36:35,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg7476a660-f0ee-4ab4-8170-38ef0998af01/GCF_015191005.1_ASM1519100v1_genomic.fna.gz | prodigal -d GCF_015191005.1_ASM1519100v1_genomic.fna/cds.fna -a GCF_015191005.1_ASM1519100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:48,989] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:48,990] [INFO] Task started: HMMsearch
[2024-01-24 12:36:48,990] [INFO] Running command: hmmsearch --tblout GCF_015191005.1_ASM1519100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/reference_markers.hmm GCF_015191005.1_ASM1519100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:49,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:49,290] [INFO] Found 6/6 markers.
[2024-01-24 12:36:49,322] [INFO] Query marker FASTA was written to GCF_015191005.1_ASM1519100v1_genomic.fna/markers.fasta
[2024-01-24 12:36:49,323] [INFO] Task started: Blastn
[2024-01-24 12:36:49,323] [INFO] Running command: blastn -query GCF_015191005.1_ASM1519100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/reference_markers.fasta -out GCF_015191005.1_ASM1519100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:49,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:49,947] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:49,947] [INFO] Target genome list was writen to GCF_015191005.1_ASM1519100v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:49,996] [INFO] Task started: fastANI
[2024-01-24 12:36:49,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg7476a660-f0ee-4ab4-8170-38ef0998af01/GCF_015191005.1_ASM1519100v1_genomic.fna.gz --refList GCF_015191005.1_ASM1519100v1_genomic.fna/target_genomes.txt --output GCF_015191005.1_ASM1519100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:59,166] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:59,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:59,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:59,191] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:59,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:59,191] [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
Kaistella antarctica	strain=NCTC13489	GCA_900637895.1	266748	266748	type	True	82.5753	704	1238	95	below_threshold
Kaistella antarctica	strain=DSM 17047	GCA_900109615.1	266748	266748	type	True	82.5243	702	1238	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	82.3605	660	1238	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	80.6629	591	1238	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	80.6373	585	1238	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	80.6166	576	1238	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	80.5983	587	1238	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	79.3176	515	1238	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	78.7423	386	1238	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.7538	260	1238	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	77.5361	270	1238	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	77.3548	227	1238	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	76.9169	66	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:59,194] [INFO] DFAST Taxonomy check result was written to GCF_015191005.1_ASM1519100v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:59,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:59,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:59,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/checkm_data
[2024-01-24 12:36:59,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:59,239] [INFO] Task started: CheckM
[2024-01-24 12:36:59,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015191005.1_ASM1519100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015191005.1_ASM1519100v1_genomic.fna/checkm_input GCF_015191005.1_ASM1519100v1_genomic.fna/checkm_result
[2024-01-24 12:37:42,278] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:42,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:42,299] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:42,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:42,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015191005.1_ASM1519100v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:42,301] [INFO] Task started: Blastn
[2024-01-24 12:37:42,301] [INFO] Running command: blastn -query GCF_015191005.1_ASM1519100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg555793f0-6b06-4f27-8f48-d767e69109f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_015191005.1_ASM1519100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:43,151] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:43,156] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:43,157] [INFO] Target genome list was writen to GCF_015191005.1_ASM1519100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:43,170] [INFO] Task started: fastANI
[2024-01-24 12:37:43,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg7476a660-f0ee-4ab4-8170-38ef0998af01/GCF_015191005.1_ASM1519100v1_genomic.fna.gz --refList GCF_015191005.1_ASM1519100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015191005.1_ASM1519100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:49,181] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:49,193] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:49,193] [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_015191005.1	s__Kaistella flava	100.0	1238	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004359195.1	s__Kaistella sp004359195	83.6281	749	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415135.1	s__Kaistella sp002415135	83.5988	757	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109615.1	s__Kaistella antarctica	82.5169	703	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003860585.1	s__Kaistella carnis	82.4019	660	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_007362475.1	s__Kaistella sp007362475	80.9834	552	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812865.1	s__Kaistella jeonii	80.647	585	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:49,195] [INFO] GTDB search result was written to GCF_015191005.1_ASM1519100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:49,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:49,198] [INFO] DFAST_QC result json was written to GCF_015191005.1_ASM1519100v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:49,198] [INFO] DFAST_QC completed!
[2024-01-24 12:37:49,199] [INFO] Total running time: 0h1m15s