[2023-06-13 21:20:32,239] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference
[2023-06-13 21:20:33,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:33,536] [INFO] Task started: Prodigal
[2023-06-13 21:20:33,536] [INFO] Running command: gunzip -c /var/lib/cwl/stge6390157-783a-443b-8f4b-5fe1c8d48dcb/GCA_022841325.1_ASM2284132v1_genomic.fna.gz | prodigal -d GCA_022841325.1_ASM2284132v1_genomic.fna/cds.fna -a GCA_022841325.1_ASM2284132v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:50,519] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:50,520] [INFO] Task started: HMMsearch
[2023-06-13 21:20:50,520] [INFO] Running command: hmmsearch --tblout GCA_022841325.1_ASM2284132v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/reference_markers.hmm GCA_022841325.1_ASM2284132v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:50,848] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:50,849] [INFO] Found 6/6 markers.
[2023-06-13 21:20:50,894] [INFO] Query marker FASTA was written to GCA_022841325.1_ASM2284132v1_genomic.fna/markers.fasta
[2023-06-13 21:20:50,894] [INFO] Task started: Blastn
[2023-06-13 21:20:50,894] [INFO] Running command: blastn -query GCA_022841325.1_ASM2284132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/reference_markers.fasta -out GCA_022841325.1_ASM2284132v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:51,726] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:51,735] [INFO] Selected 31 target genomes.
[2023-06-13 21:20:51,735] [INFO] Target genome list was writen to GCA_022841325.1_ASM2284132v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:51,737] [INFO] Task started: fastANI
[2023-06-13 21:20:51,737] [INFO] Running command: fastANI --query /var/lib/cwl/stge6390157-783a-443b-8f4b-5fe1c8d48dcb/GCA_022841325.1_ASM2284132v1_genomic.fna.gz --refList GCA_022841325.1_ASM2284132v1_genomic.fna/target_genomes.txt --output GCA_022841325.1_ASM2284132v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:21:11,815] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:11,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:21:11,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:21:11,833] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:21:11,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:21:11,834] [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
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	77.0054	273	1856	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	76.9887	231	1856	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	76.8896	207	1856	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.8713	219	1856	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	76.8632	224	1856	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.8581	224	1856	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.8454	215	1856	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.8414	201	1856	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.8331	226	1856	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.829	234	1856	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	76.8216	241	1856	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.8058	241	1856	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	76.7939	182	1856	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.7258	256	1856	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.5794	215	1856	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.5413	254	1856	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	76.5056	198	1856	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	76.4968	196	1856	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.4763	299	1856	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	76.4744	223	1856	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.4232	223	1856	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.391	213	1856	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	76.329	176	1856	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	76.255	161	1856	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.8066	131	1856	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.7789	136	1856	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	75.5585	164	1856	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	75.5337	81	1856	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	75.5113	166	1856	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	75.4548	87	1856	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	75.1974	102	1856	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:21:11,836] [INFO] DFAST Taxonomy check result was written to GCA_022841325.1_ASM2284132v1_genomic.fna/tc_result.tsv
[2023-06-13 21:21:11,837] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:21:11,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:21:11,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/checkm_data
[2023-06-13 21:21:11,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:21:11,895] [INFO] Task started: CheckM
[2023-06-13 21:21:11,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022841325.1_ASM2284132v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022841325.1_ASM2284132v1_genomic.fna/checkm_input GCA_022841325.1_ASM2284132v1_genomic.fna/checkm_result
[2023-06-13 21:22:07,320] [INFO] Task succeeded: CheckM
[2023-06-13 21:22:07,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:22:07,342] [INFO] ===== Completeness check finished =====
[2023-06-13 21:22:07,342] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:22:07,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022841325.1_ASM2284132v1_genomic.fna/markers.fasta)
[2023-06-13 21:22:07,344] [INFO] Task started: Blastn
[2023-06-13 21:22:07,344] [INFO] Running command: blastn -query GCA_022841325.1_ASM2284132v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdceca92e-e185-44df-896b-51f77f359f0f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022841325.1_ASM2284132v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:22:08,921] [INFO] Task succeeded: Blastn
[2023-06-13 21:22:08,924] [INFO] Selected 21 target genomes.
[2023-06-13 21:22:08,924] [INFO] Target genome list was writen to GCA_022841325.1_ASM2284132v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:22:08,972] [INFO] Task started: fastANI
[2023-06-13 21:22:08,972] [INFO] Running command: fastANI --query /var/lib/cwl/stge6390157-783a-443b-8f4b-5fe1c8d48dcb/GCA_022841325.1_ASM2284132v1_genomic.fna.gz --refList GCA_022841325.1_ASM2284132v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022841325.1_ASM2284132v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:22:22,776] [INFO] Task succeeded: fastANI
[2023-06-13 21:22:22,789] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:22:22,789] [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
GCA_016717705.1	s__JADKFD01 sp016717705	80.2251	798	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713135.1	s__JADKFD01 sp016713135	79.9242	836	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187485.1	s__JADKFD01 sp019187485	79.6668	674	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101825.1	s__Aquimonas voraii	77.2985	318	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202935.1	s__Rehaibacterium terrae	77.214	254	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182785.1	s__JADKHK01 sp016182785	76.9771	271	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018334015.1	s__Silanimonas sp018334015	76.9458	175	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	99.95	99.95	0.95	0.95	2	-
GCF_000761445.1	s__Oleiagrimonas soli	76.8787	222	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	76.8331	279	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395255.1	s__Oleiagrimonas citrea	76.8049	181	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	98.37	98.37	0.90	0.90	2	-
GCA_004297225.1	s__Luteimonas_B sp004297225	76.6843	168	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	76.6734	237	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	76.5757	241	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077135.1	s__Metallibacterium scheffleri	76.4573	200	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Metallibacterium	95.0	98.26	96.51	0.97	0.94	3	-
GCA_002483055.1	s__Dokdonella sp002483055	76.4143	243	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014338185.1	s__Dokdonella_A sp014338185	76.3715	205	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	96.24	96.24	0.88	0.88	2	-
GCF_003148905.1	s__Fulvimonas soli	76.3124	278	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000801295.1	s__MONJU sp000801295	76.0301	86	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377905.1	s__Thioalkalivibrio sp000377905	75.9842	82	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051615.1	s__HyVt-448 sp011051615	75.7566	71	1856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__HyVt-448	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:22:22,791] [INFO] GTDB search result was written to GCA_022841325.1_ASM2284132v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:22:22,792] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:22:22,796] [INFO] DFAST_QC result json was written to GCA_022841325.1_ASM2284132v1_genomic.fna/dqc_result.json
[2023-06-13 21:22:22,796] [INFO] DFAST_QC completed!
[2023-06-13 21:22:22,796] [INFO] Total running time: 0h1m51s