[2024-01-24 13:22:25,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference
[2024-01-24 13:22:26,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,819] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg24f2fde7-1e1a-4abb-b0ea-f6e756b515a8/GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/cds.fna -a GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:35,535] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:35,535] [INFO] Task started: HMMsearch
[2024-01-24 13:22:35,536] [INFO] Running command: hmmsearch --tblout GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/reference_markers.hmm GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:35,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:35,804] [INFO] Found 6/6 markers.
[2024-01-24 13:22:35,832] [INFO] Query marker FASTA was written to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:35,833] [INFO] Task started: Blastn
[2024-01-24 13:22:35,833] [INFO] Running command: blastn -query GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/reference_markers.fasta -out GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:36,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:36,465] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:36,465] [INFO] Target genome list was writen to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:36,539] [INFO] Task started: fastANI
[2024-01-24 13:22:36,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg24f2fde7-1e1a-4abb-b0ea-f6e756b515a8/GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna.gz --refList GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:45,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:45,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:45,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:45,307] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:45,307] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:45,307] [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 treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	100.0	785	787	95	inconclusive
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	95.8632	722	787	95	inconclusive
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	88.0228	688	787	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	79.0353	389	787	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	78.661	323	787	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.5572	316	787	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	78.5026	309	787	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	78.4794	312	787	95	below_threshold
Kaistella antarctica	strain=DSM 17047	GCA_900109615.1	266748	266748	type	True	78.4128	334	787	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	78.2892	323	787	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	77.7002	222	787	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	77.3562	167	787	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	76.8652	153	787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:45,309] [INFO] DFAST Taxonomy check result was written to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:45,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:45,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:45,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/checkm_data
[2024-01-24 13:22:45,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:45,338] [INFO] Task started: CheckM
[2024-01-24 13:22:45,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/checkm_input GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:13,789] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:13,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:13,805] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:13,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:13,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:13,805] [INFO] Task started: Blastn
[2024-01-24 13:23:13,806] [INFO] Running command: blastn -query GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgca27d0db-35a6-4e2e-b965-e83c0a1b2bd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:14,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:14,635] [INFO] Selected 15 target genomes.
[2024-01-24 13:23:14,635] [INFO] Target genome list was writen to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:14,644] [INFO] Task started: fastANI
[2024-01-24 13:23:14,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg24f2fde7-1e1a-4abb-b0ea-f6e756b515a8/GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna.gz --refList GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:22,926] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:22,935] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:22,935] [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_900114045.1	s__Kaistella treverensis	100.0	785	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.8987	N/A	N/A	N/A	N/A	1	conclusive
GCF_000812875.1	s__Kaistella solincola	95.8632	722	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.8987	N/A	N/A	N/A	N/A	1	-
GCF_003860505.1	s__Kaistella daneshvariae	88.0228	688	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.86	0.91	0.91	2	-
GCA_002453895.1	s__Kaistella sp002453895	79.0756	295	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003860585.1	s__Kaistella carnis	79.0353	389	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_004359195.1	s__Kaistella sp004359195	78.9343	392	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015191005.1	s__Kaistella flava	78.8606	393	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002197835.1	s__Kaistella sp002197835	78.7564	303	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCF_900156725.1	s__Kaistella chaponensis	78.6796	321	787	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	78.6366	373	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007362475.1	s__Kaistella sp007362475	78.6153	311	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902795.1	s__Kaistella sp018902795	78.585	328	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679325.1	s__Kaistella gelatinilytica	78.544	317	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000023725.1	s__Kaistella sp000023725	77.8988	239	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426785.1	s__Kaistella sp002426785	77.7542	251	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,937] [INFO] GTDB search result was written to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:22,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:22,940] [INFO] DFAST_QC result json was written to GCF_900114045.1_IMG-taxon_2687453775_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:22,940] [INFO] DFAST_QC completed!
[2024-01-24 13:23:22,941] [INFO] Total running time: 0h0m57s