[2024-01-24 13:40:55,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference
[2024-01-24 13:40:56,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,501] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgda98fe85-bb53-4645-9cbc-7e55139434e2/GCF_017742245.1_ASM1774224v1_genomic.fna.gz | prodigal -d GCF_017742245.1_ASM1774224v1_genomic.fna/cds.fna -a GCF_017742245.1_ASM1774224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:31,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:31,865] [INFO] Task started: HMMsearch
[2024-01-24 13:41:31,866] [INFO] Running command: hmmsearch --tblout GCF_017742245.1_ASM1774224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/reference_markers.hmm GCF_017742245.1_ASM1774224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:32,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:32,237] [INFO] Found 6/6 markers.
[2024-01-24 13:41:32,303] [INFO] Query marker FASTA was written to GCF_017742245.1_ASM1774224v1_genomic.fna/markers.fasta
[2024-01-24 13:41:32,303] [INFO] Task started: Blastn
[2024-01-24 13:41:32,303] [INFO] Running command: blastn -query GCF_017742245.1_ASM1774224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/reference_markers.fasta -out GCF_017742245.1_ASM1774224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,893] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:32,893] [INFO] Target genome list was writen to GCF_017742245.1_ASM1774224v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:32,897] [INFO] Task started: fastANI
[2024-01-24 13:41:32,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgda98fe85-bb53-4645-9cbc-7e55139434e2/GCF_017742245.1_ASM1774224v1_genomic.fna.gz --refList GCF_017742245.1_ASM1774224v1_genomic.fna/target_genomes.txt --output GCF_017742245.1_ASM1774224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,131] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,140] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:50,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,140] [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 soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	100.0	2944	2946	95	conclusive
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	84.3741	1904	2946	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	84.3551	1929	2946	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	83.735	1944	2946	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	83.6948	1968	2946	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.183	78	2946	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.0424	91	2946	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.896	80	2946	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	75.7333	90	2946	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.5554	79	2946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,141] [INFO] DFAST Taxonomy check result was written to GCF_017742245.1_ASM1774224v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/checkm_data
[2024-01-24 13:41:50,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,223] [INFO] Task started: CheckM
[2024-01-24 13:41:50,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017742245.1_ASM1774224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017742245.1_ASM1774224v1_genomic.fna/checkm_input GCF_017742245.1_ASM1774224v1_genomic.fna/checkm_result
[2024-01-24 13:43:22,833] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:22,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:22,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:22,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:22,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017742245.1_ASM1774224v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:22,852] [INFO] Task started: Blastn
[2024-01-24 13:43:22,852] [INFO] Running command: blastn -query GCF_017742245.1_ASM1774224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907b1014-4065-42b7-b406-a2b78e080393/dqc_reference/reference_markers_gtdb.fasta -out GCF_017742245.1_ASM1774224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:23,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:23,595] [INFO] Selected 14 target genomes.
[2024-01-24 13:43:23,596] [INFO] Target genome list was writen to GCF_017742245.1_ASM1774224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:23,661] [INFO] Task started: fastANI
[2024-01-24 13:43:23,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgda98fe85-bb53-4645-9cbc-7e55139434e2/GCF_017742245.1_ASM1774224v1_genomic.fna.gz --refList GCF_017742245.1_ASM1774224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017742245.1_ASM1774224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:43,638] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:43,646] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:43,646] [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_017742245.1	s__Niastella sp017742245	100.0	2944	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110245.1	s__Niastella yeongjuensis	84.3466	1931	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000246855.1	s__Niastella koreensis	83.6853	1970	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002077945.1	s__Niastella vici	80.8829	1472	2946	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	80.7941	1261	2946	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	80.5196	1251	2946	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	80.4831	1453	2946	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	80.2153	1320	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243445.1	s__46-32 sp003243445	76.3418	101	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.2022	77	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720825.1	s__JJ008 sp016720825	76.134	80	2946	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.65	98.65	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:43,647] [INFO] GTDB search result was written to GCF_017742245.1_ASM1774224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:43,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:43,653] [INFO] DFAST_QC result json was written to GCF_017742245.1_ASM1774224v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:43,653] [INFO] DFAST_QC completed!
[2024-01-24 13:43:43,653] [INFO] Total running time: 0h2m48s