[2024-01-24 12:15:18,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference
[2024-01-24 12:15:20,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,331] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb53dd51-c959-46c6-81bc-89ab553d3195/GCF_030409525.1_ASM3040952v1_genomic.fna.gz | prodigal -d GCF_030409525.1_ASM3040952v1_genomic.fna/cds.fna -a GCF_030409525.1_ASM3040952v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,161] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,161] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,161] [INFO] Running command: hmmsearch --tblout GCF_030409525.1_ASM3040952v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/reference_markers.hmm GCF_030409525.1_ASM3040952v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:33,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:33,407] [INFO] Found 6/6 markers.
[2024-01-24 12:15:33,437] [INFO] Query marker FASTA was written to GCF_030409525.1_ASM3040952v1_genomic.fna/markers.fasta
[2024-01-24 12:15:33,437] [INFO] Task started: Blastn
[2024-01-24 12:15:33,438] [INFO] Running command: blastn -query GCF_030409525.1_ASM3040952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/reference_markers.fasta -out GCF_030409525.1_ASM3040952v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:34,062] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:34,066] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:34,067] [INFO] Target genome list was writen to GCF_030409525.1_ASM3040952v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:34,073] [INFO] Task started: fastANI
[2024-01-24 12:15:34,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb53dd51-c959-46c6-81bc-89ab553d3195/GCF_030409525.1_ASM3040952v1_genomic.fna.gz --refList GCF_030409525.1_ASM3040952v1_genomic.fna/target_genomes.txt --output GCF_030409525.1_ASM3040952v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:42,742] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:42,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:42,758] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:42,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:42,758] [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	80.4718	590	1051	95	below_threshold
Kaistella antarctica	strain=DSM 17047	GCA_900109615.1	266748	266748	type	True	80.457	596	1051	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	80.2617	531	1051	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	79.2151	438	1051	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	78.9832	439	1051	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	78.9725	444	1051	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	78.9314	436	1051	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.8498	442	1051	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	78.5174	331	1051	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	78.4044	333	1051	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.135	253	1051	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	76.9635	184	1051	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	76.9158	204	1051	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	76.719	183	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,760] [INFO] DFAST Taxonomy check result was written to GCF_030409525.1_ASM3040952v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:42,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:42,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:42,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/checkm_data
[2024-01-24 12:15:42,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,795] [INFO] Task started: CheckM
[2024-01-24 12:15:42,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409525.1_ASM3040952v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409525.1_ASM3040952v1_genomic.fna/checkm_input GCF_030409525.1_ASM3040952v1_genomic.fna/checkm_result
[2024-01-24 12:16:23,253] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:23,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:23,280] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:23,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:23,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409525.1_ASM3040952v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:23,281] [INFO] Task started: Blastn
[2024-01-24 12:16:23,281] [INFO] Running command: blastn -query GCF_030409525.1_ASM3040952v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc808a15-6a63-4f56-a600-467e483a4fd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409525.1_ASM3040952v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:24,098] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:24,102] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:24,102] [INFO] Target genome list was writen to GCF_030409525.1_ASM3040952v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:24,110] [INFO] Task started: fastANI
[2024-01-24 12:16:24,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb53dd51-c959-46c6-81bc-89ab553d3195/GCF_030409525.1_ASM3040952v1_genomic.fna.gz --refList GCF_030409525.1_ASM3040952v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409525.1_ASM3040952v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:30,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:30,893] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:30,894] [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	81.3193	657	1051	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	81.3048	652	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359195.1	s__Kaistella sp004359195	81.0433	596	1051	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	80.457	596	1051	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	80.2647	530	1051	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	79.6439	446	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156725.1	s__Kaistella chaponensis	79.2043	439	1051	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	78.983	439	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_015679325.1	s__Kaistella gelatinilytica	78.8698	440	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507325.1	s__Chryseobacterium greenlandense	76.9158	204	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:30,896] [INFO] GTDB search result was written to GCF_030409525.1_ASM3040952v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:30,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:30,901] [INFO] DFAST_QC result json was written to GCF_030409525.1_ASM3040952v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:30,901] [INFO] DFAST_QC completed!
[2024-01-24 12:16:30,901] [INFO] Total running time: 0h1m12s