[2024-01-25 18:42:20,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference
[2024-01-25 18:42:21,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,766] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgf39626ee-ebd6-43a9-93ac-49a4114ed86c/GCF_015679325.1_ASM1567932v1_genomic.fna.gz | prodigal -d GCF_015679325.1_ASM1567932v1_genomic.fna/cds.fna -a GCF_015679325.1_ASM1567932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:32,133] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:32,133] [INFO] Task started: HMMsearch
[2024-01-25 18:42:32,133] [INFO] Running command: hmmsearch --tblout GCF_015679325.1_ASM1567932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/reference_markers.hmm GCF_015679325.1_ASM1567932v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:32,335] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:32,336] [INFO] Found 6/6 markers.
[2024-01-25 18:42:32,362] [INFO] Query marker FASTA was written to GCF_015679325.1_ASM1567932v1_genomic.fna/markers.fasta
[2024-01-25 18:42:32,362] [INFO] Task started: Blastn
[2024-01-25 18:42:32,362] [INFO] Running command: blastn -query GCF_015679325.1_ASM1567932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/reference_markers.fasta -out GCF_015679325.1_ASM1567932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:32,952] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:32,955] [INFO] Selected 12 target genomes.
[2024-01-25 18:42:32,956] [INFO] Target genome list was writen to GCF_015679325.1_ASM1567932v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:32,961] [INFO] Task started: fastANI
[2024-01-25 18:42:32,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgf39626ee-ebd6-43a9-93ac-49a4114ed86c/GCF_015679325.1_ASM1567932v1_genomic.fna.gz --refList GCF_015679325.1_ASM1567932v1_genomic.fna/target_genomes.txt --output GCF_015679325.1_ASM1567932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:40,523] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:40,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:40,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:40,532] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:40,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:40,532] [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 gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	100.0	1069	1069	95	conclusive
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	91.0403	904	1069	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	91.0179	916	1069	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	90.9715	905	1069	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	82.5305	699	1069	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	80.2097	512	1069	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.7342	350	1069	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	78.0968	356	1069	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	78.08	357	1069	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	77.6318	214	1069	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.2152	239	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:40,534] [INFO] DFAST Taxonomy check result was written to GCF_015679325.1_ASM1567932v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:40,534] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:40,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:40,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/checkm_data
[2024-01-25 18:42:40,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:40,572] [INFO] Task started: CheckM
[2024-01-25 18:42:40,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015679325.1_ASM1567932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015679325.1_ASM1567932v1_genomic.fna/checkm_input GCF_015679325.1_ASM1567932v1_genomic.fna/checkm_result
[2024-01-25 18:43:14,562] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:14,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:14,587] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:14,588] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:14,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015679325.1_ASM1567932v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:14,588] [INFO] Task started: Blastn
[2024-01-25 18:43:14,588] [INFO] Running command: blastn -query GCF_015679325.1_ASM1567932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e1128b8-9f6c-498d-a2db-595f5ab5cdda/dqc_reference/reference_markers_gtdb.fasta -out GCF_015679325.1_ASM1567932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:15,403] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:15,405] [INFO] Selected 12 target genomes.
[2024-01-25 18:43:15,406] [INFO] Target genome list was writen to GCF_015679325.1_ASM1567932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:15,412] [INFO] Task started: fastANI
[2024-01-25 18:43:15,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgf39626ee-ebd6-43a9-93ac-49a4114ed86c/GCF_015679325.1_ASM1567932v1_genomic.fna.gz --refList GCF_015679325.1_ASM1567932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015679325.1_ASM1567932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:24,283] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:24,291] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:24,292] [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_015679325.1	s__Kaistella gelatinilytica	100.0	1069	1069	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_000812865.1	s__Kaistella jeonii	90.9715	905	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900156725.1	s__Kaistella chaponensis	82.5327	699	1069	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	80.5974	587	1069	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	79.7986	543	1069	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	79.5424	482	1069	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	79.5337	407	1069	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	79.3949	523	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000735695.2	s__Kaistella haifensis	78.1569	333	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCA_002426785.1	s__Kaistella sp002426785	78.1405	340	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	77.5849	215	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_016595215.1	s__Chryseobacterium sp016595215	76.5455	172	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:24,293] [INFO] GTDB search result was written to GCF_015679325.1_ASM1567932v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:24,293] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:24,296] [INFO] DFAST_QC result json was written to GCF_015679325.1_ASM1567932v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:24,296] [INFO] DFAST_QC completed!
[2024-01-25 18:43:24,296] [INFO] Total running time: 0h1m4s