[2024-01-24 13:40:45,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,781] [INFO] DQC Reference Directory: /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference
[2024-01-24 13:40:47,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,080] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg328fbd36-08e3-4532-9dd8-df920f2e8261/GCF_002077935.1_ASM207793v1_genomic.fna.gz | prodigal -d GCF_002077935.1_ASM207793v1_genomic.fna/cds.fna -a GCF_002077935.1_ASM207793v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:27,918] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:27,919] [INFO] Task started: HMMsearch
[2024-01-24 13:41:27,919] [INFO] Running command: hmmsearch --tblout GCF_002077935.1_ASM207793v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/reference_markers.hmm GCF_002077935.1_ASM207793v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:28,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:28,300] [INFO] Found 6/6 markers.
[2024-01-24 13:41:28,363] [INFO] Query marker FASTA was written to GCF_002077935.1_ASM207793v1_genomic.fna/markers.fasta
[2024-01-24 13:41:28,364] [INFO] Task started: Blastn
[2024-01-24 13:41:28,364] [INFO] Running command: blastn -query GCF_002077935.1_ASM207793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/reference_markers.fasta -out GCF_002077935.1_ASM207793v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:28,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:28,982] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:28,982] [INFO] Target genome list was writen to GCF_002077935.1_ASM207793v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,100] [INFO] Task started: fastANI
[2024-01-24 13:41:29,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg328fbd36-08e3-4532-9dd8-df920f2e8261/GCF_002077935.1_ASM207793v1_genomic.fna.gz --refList GCF_002077935.1_ASM207793v1_genomic.fna/target_genomes.txt --output GCF_002077935.1_ASM207793v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:44,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:44,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:44,154] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:44,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:44,154] [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
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	100.0	2806	2807	95	conclusive
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	99.9932	2804	2807	95	conclusive
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	85.0314	1886	2807	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	85.0026	1889	2807	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	84.2884	1940	2807	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.1868	79	2807	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0736	90	2807	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	76.0155	66	2807	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.8934	70	2807	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.8285	94	2807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,156] [INFO] DFAST Taxonomy check result was written to GCF_002077935.1_ASM207793v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:44,156] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:44,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:44,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/checkm_data
[2024-01-24 13:41:44,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:44,233] [INFO] Task started: CheckM
[2024-01-24 13:41:44,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002077935.1_ASM207793v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002077935.1_ASM207793v1_genomic.fna/checkm_input GCF_002077935.1_ASM207793v1_genomic.fna/checkm_result
[2024-01-24 13:43:31,618] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:31,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:31,643] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:31,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:31,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002077935.1_ASM207793v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:31,644] [INFO] Task started: Blastn
[2024-01-24 13:43:31,644] [INFO] Running command: blastn -query GCF_002077935.1_ASM207793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30f7c81-2633-4d9e-8fef-b98b8a54c420/dqc_reference/reference_markers_gtdb.fasta -out GCF_002077935.1_ASM207793v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:32,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:32,417] [INFO] Selected 8 target genomes.
[2024-01-24 13:43:32,418] [INFO] Target genome list was writen to GCF_002077935.1_ASM207793v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:32,537] [INFO] Task started: fastANI
[2024-01-24 13:43:32,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg328fbd36-08e3-4532-9dd8-df920f2e8261/GCF_002077935.1_ASM207793v1_genomic.fna.gz --refList GCF_002077935.1_ASM207793v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002077935.1_ASM207793v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:47,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:47,944] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:47,944] [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_900110245.1	s__Niastella yeongjuensis	99.9985	2803	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000246855.1	s__Niastella koreensis	85.037	1885	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017742245.1	s__Niastella sp017742245	84.2884	1940	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077945.1	s__Niastella vici	81.1129	1388	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	80.7576	1391	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004834005.1	s__Niastella caeni	80.756	1262	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	80.6403	1249	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	80.5123	1292	2807	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:47,946] [INFO] GTDB search result was written to GCF_002077935.1_ASM207793v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:47,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:47,950] [INFO] DFAST_QC result json was written to GCF_002077935.1_ASM207793v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:47,950] [INFO] DFAST_QC completed!
[2024-01-24 13:43:47,950] [INFO] Total running time: 0h3m2s