[2024-01-24 13:41:25,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference
[2024-01-24 13:41:26,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:26,620] [INFO] Task started: Prodigal
[2024-01-24 13:41:26,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dfdd0ff-3534-4d49-a4c0-74cadeb5eade/GCF_004336905.1_ASM433690v1_genomic.fna.gz | prodigal -d GCF_004336905.1_ASM433690v1_genomic.fna/cds.fna -a GCF_004336905.1_ASM433690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:56,771] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:56,771] [INFO] Task started: HMMsearch
[2024-01-24 13:41:56,771] [INFO] Running command: hmmsearch --tblout GCF_004336905.1_ASM433690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/reference_markers.hmm GCF_004336905.1_ASM433690v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:57,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:57,165] [INFO] Found 6/6 markers.
[2024-01-24 13:41:57,234] [INFO] Query marker FASTA was written to GCF_004336905.1_ASM433690v1_genomic.fna/markers.fasta
[2024-01-24 13:41:57,234] [INFO] Task started: Blastn
[2024-01-24 13:41:57,234] [INFO] Running command: blastn -query GCF_004336905.1_ASM433690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/reference_markers.fasta -out GCF_004336905.1_ASM433690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,500] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,505] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:58,505] [INFO] Target genome list was writen to GCF_004336905.1_ASM433690v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:58,528] [INFO] Task started: fastANI
[2024-01-24 13:41:58,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dfdd0ff-3534-4d49-a4c0-74cadeb5eade/GCF_004336905.1_ASM433690v1_genomic.fna.gz --refList GCF_004336905.1_ASM433690v1_genomic.fna/target_genomes.txt --output GCF_004336905.1_ASM433690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:14,967] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:14,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:14,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:14,985] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:14,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:14,986] [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
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	84.2487	1020	2720	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	83.9155	1068	2720	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	83.8507	1049	2720	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	83.6166	1050	2720	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	83.6057	894	2720	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	82.7635	859	2720	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	82.69	795	2720	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	81.6575	765	2720	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	81.6046	766	2720	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	81.5143	761	2720	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	81.1206	778	2720	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.0323	798	2720	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	79.9827	680	2720	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.2625	501	2720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:14,987] [INFO] DFAST Taxonomy check result was written to GCF_004336905.1_ASM433690v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:14,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:14,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:14,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/checkm_data
[2024-01-24 13:42:14,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:15,065] [INFO] Task started: CheckM
[2024-01-24 13:42:15,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004336905.1_ASM433690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004336905.1_ASM433690v1_genomic.fna/checkm_input GCF_004336905.1_ASM433690v1_genomic.fna/checkm_result
[2024-01-24 13:44:10,121] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:10,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 100.00%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-24 13:44:10,164] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:10,165] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:10,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004336905.1_ASM433690v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:10,166] [INFO] Task started: Blastn
[2024-01-24 13:44:10,166] [INFO] Running command: blastn -query GCF_004336905.1_ASM433690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ba2875-4045-4eac-80a5-e7795be79ca6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004336905.1_ASM433690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:12,704] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:12,709] [INFO] Selected 17 target genomes.
[2024-01-24 13:44:12,709] [INFO] Target genome list was writen to GCF_004336905.1_ASM433690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:12,734] [INFO] Task started: fastANI
[2024-01-24 13:44:12,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dfdd0ff-3534-4d49-a4c0-74cadeb5eade/GCF_004336905.1_ASM433690v1_genomic.fna.gz --refList GCF_004336905.1_ASM433690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004336905.1_ASM433690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:35,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:36,037] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:36,037] [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_004322705.1	s__Dyella terrae	99.8974	1410	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003332825.1	s__Dyella sp003332825	84.5241	996	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	84.2281	1023	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	84.1904	1046	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	84.1727	1038	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003264855.1	s__Dyella jiangningensis_C	83.9409	1084	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	83.9374	1065	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	83.8537	1049	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	83.6318	1048	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010355.1	s__Dyella japonica	83.5924	895	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725385.1	s__Dyella japonica_C	83.5317	1069	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000632805.1	s__Dyella jiangningensis	83.5274	1113	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	83.4789	979	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012275375.1	s__Dyella sp012275375	83.4367	997	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_003688835.1	s__Dyella sp003688835	83.4161	1056	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	83.199	1005	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	81.8532	825	2720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:36,052] [INFO] GTDB search result was written to GCF_004336905.1_ASM433690v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:36,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:36,058] [INFO] DFAST_QC result json was written to GCF_004336905.1_ASM433690v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:36,059] [INFO] DFAST_QC completed!
[2024-01-24 13:44:36,059] [INFO] Total running time: 0h3m11s