[2024-01-25 19:11:35,671] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference
[2024-01-25 19:11:36,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,885] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg6adec075-c36e-4851-bb51-9068f15b517c/GCF_000246855.1_ASM24685v1_genomic.fna.gz | prodigal -d GCF_000246855.1_ASM24685v1_genomic.fna/cds.fna -a GCF_000246855.1_ASM24685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:15,675] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:15,676] [INFO] Task started: HMMsearch
[2024-01-25 19:12:15,676] [INFO] Running command: hmmsearch --tblout GCF_000246855.1_ASM24685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/reference_markers.hmm GCF_000246855.1_ASM24685v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:16,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:16,002] [INFO] Found 6/6 markers.
[2024-01-25 19:12:16,066] [INFO] Query marker FASTA was written to GCF_000246855.1_ASM24685v1_genomic.fna/markers.fasta
[2024-01-25 19:12:16,066] [INFO] Task started: Blastn
[2024-01-25 19:12:16,066] [INFO] Running command: blastn -query GCF_000246855.1_ASM24685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/reference_markers.fasta -out GCF_000246855.1_ASM24685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:16,605] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:16,607] [INFO] Selected 11 target genomes.
[2024-01-25 19:12:16,608] [INFO] Target genome list was writen to GCF_000246855.1_ASM24685v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:16,612] [INFO] Task started: fastANI
[2024-01-25 19:12:16,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg6adec075-c36e-4851-bb51-9068f15b517c/GCF_000246855.1_ASM24685v1_genomic.fna.gz --refList GCF_000246855.1_ASM24685v1_genomic.fna/target_genomes.txt --output GCF_000246855.1_ASM24685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:35,586] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:35,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:35,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:35,596] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:12:35,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:35,596] [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 koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	100.0	3011	3011	95	conclusive
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	99.9854	2963	3011	95	conclusive
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	84.9082	1926	3011	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	84.8929	1905	3011	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	83.734	1963	3011	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	81.0554	1604	3011	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.4459	65	3011	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.2848	91	3011	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.9699	106	3011	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.8986	103	3011	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.6526	92	3011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:35,600] [INFO] DFAST Taxonomy check result was written to GCF_000246855.1_ASM24685v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:35,604] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:35,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:35,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/checkm_data
[2024-01-25 19:12:35,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:35,688] [INFO] Task started: CheckM
[2024-01-25 19:12:35,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000246855.1_ASM24685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000246855.1_ASM24685v1_genomic.fna/checkm_input GCF_000246855.1_ASM24685v1_genomic.fna/checkm_result
[2024-01-25 19:14:19,063] [INFO] Task succeeded: CheckM
[2024-01-25 19:14:19,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:14:19,086] [INFO] ===== Completeness check finished =====
[2024-01-25 19:14:19,086] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:14:19,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000246855.1_ASM24685v1_genomic.fna/markers.fasta)
[2024-01-25 19:14:19,087] [INFO] Task started: Blastn
[2024-01-25 19:14:19,087] [INFO] Running command: blastn -query GCF_000246855.1_ASM24685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c19287-223d-4a2c-a3c5-895a618a108d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000246855.1_ASM24685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:14:19,897] [INFO] Task succeeded: Blastn
[2024-01-25 19:14:19,900] [INFO] Selected 8 target genomes.
[2024-01-25 19:14:19,900] [INFO] Target genome list was writen to GCF_000246855.1_ASM24685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:14:19,924] [INFO] Task started: fastANI
[2024-01-25 19:14:19,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg6adec075-c36e-4851-bb51-9068f15b517c/GCF_000246855.1_ASM24685v1_genomic.fna.gz --refList GCF_000246855.1_ASM24685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000246855.1_ASM24685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:36,787] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:36,794] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:36,794] [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_000246855.1	s__Niastella koreensis	100.0	3011	3011	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_900110245.1	s__Niastella yeongjuensis	84.9135	1925	3011	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	83.7264	1965	3011	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	81.0516	1604	3011	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	80.8248	1552	3011	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	80.6532	1353	3011	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	80.4317	1375	3011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924755.1	s__Niastella sp016924755	80.2183	1285	3011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:36,796] [INFO] GTDB search result was written to GCF_000246855.1_ASM24685v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:36,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:36,800] [INFO] DFAST_QC result json was written to GCF_000246855.1_ASM24685v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:36,800] [INFO] DFAST_QC completed!
[2024-01-25 19:14:36,800] [INFO] Total running time: 0h3m1s