[2023-06-27 15:01:07,672] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:01:07,676] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:01:07,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference
[2023-06-27 15:01:09,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:01:09,488] [INFO] Task started: Prodigal
[2023-06-27 15:01:09,488] [INFO] Running command: gunzip -c /var/lib/cwl/stga47ffcfe-4619-41a2-a30d-a29037ddd8ed/GCA_026193295.1_ASM2619329v1_genomic.fna.gz | prodigal -d GCA_026193295.1_ASM2619329v1_genomic.fna/cds.fna -a GCA_026193295.1_ASM2619329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:01:17,504] [INFO] Task succeeded: Prodigal
[2023-06-27 15:01:17,504] [INFO] Task started: HMMsearch
[2023-06-27 15:01:17,504] [INFO] Running command: hmmsearch --tblout GCA_026193295.1_ASM2619329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/reference_markers.hmm GCA_026193295.1_ASM2619329v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:01:17,770] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:01:17,771] [INFO] Found 6/6 markers.
[2023-06-27 15:01:17,814] [INFO] Query marker FASTA was written to GCA_026193295.1_ASM2619329v1_genomic.fna/markers.fasta
[2023-06-27 15:01:17,815] [INFO] Task started: Blastn
[2023-06-27 15:01:17,815] [INFO] Running command: blastn -query GCA_026193295.1_ASM2619329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/reference_markers.fasta -out GCA_026193295.1_ASM2619329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:18,690] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:18,694] [INFO] Selected 30 target genomes.
[2023-06-27 15:01:18,695] [INFO] Target genome list was writen to GCA_026193295.1_ASM2619329v1_genomic.fna/target_genomes.txt
[2023-06-27 15:01:18,705] [INFO] Task started: fastANI
[2023-06-27 15:01:18,706] [INFO] Running command: fastANI --query /var/lib/cwl/stga47ffcfe-4619-41a2-a30d-a29037ddd8ed/GCA_026193295.1_ASM2619329v1_genomic.fna.gz --refList GCA_026193295.1_ASM2619329v1_genomic.fna/target_genomes.txt --output GCA_026193295.1_ASM2619329v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:01:38,293] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:38,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:01:38,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:01:38,317] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:01:38,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:01:38,318] [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
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	76.8076	68	787	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.4703	60	787	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.4703	60	787	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	76.3542	71	787	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.3278	57	787	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	76.3169	67	787	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	76.3169	67	787	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.3159	70	787	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	76.2519	72	787	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.2167	64	787	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.198	58	787	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	76.1334	74	787	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.06	82	787	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	76.0457	74	787	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.037	60	787	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.9537	61	787	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	75.9451	82	787	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.9334	54	787	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	75.9235	69	787	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	75.8903	71	787	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	75.8474	62	787	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	75.7935	55	787	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	75.6808	70	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:01:38,320] [INFO] DFAST Taxonomy check result was written to GCA_026193295.1_ASM2619329v1_genomic.fna/tc_result.tsv
[2023-06-27 15:01:38,320] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:01:38,320] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:01:38,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/checkm_data
[2023-06-27 15:01:38,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:01:38,361] [INFO] Task started: CheckM
[2023-06-27 15:01:38,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026193295.1_ASM2619329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026193295.1_ASM2619329v1_genomic.fna/checkm_input GCA_026193295.1_ASM2619329v1_genomic.fna/checkm_result
[2023-06-27 15:02:06,381] [INFO] Task succeeded: CheckM
[2023-06-27 15:02:06,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:02:06,413] [INFO] ===== Completeness check finished =====
[2023-06-27 15:02:06,413] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:02:06,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026193295.1_ASM2619329v1_genomic.fna/markers.fasta)
[2023-06-27 15:02:06,414] [INFO] Task started: Blastn
[2023-06-27 15:02:06,414] [INFO] Running command: blastn -query GCA_026193295.1_ASM2619329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3249b5d2-cef1-4025-b4a5-183ed27a5646/dqc_reference/reference_markers_gtdb.fasta -out GCA_026193295.1_ASM2619329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:02:07,953] [INFO] Task succeeded: Blastn
[2023-06-27 15:02:07,958] [INFO] Selected 29 target genomes.
[2023-06-27 15:02:07,958] [INFO] Target genome list was writen to GCA_026193295.1_ASM2619329v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:02:07,978] [INFO] Task started: fastANI
[2023-06-27 15:02:07,978] [INFO] Running command: fastANI --query /var/lib/cwl/stga47ffcfe-4619-41a2-a30d-a29037ddd8ed/GCA_026193295.1_ASM2619329v1_genomic.fna.gz --refList GCA_026193295.1_ASM2619329v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026193295.1_ASM2619329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:02:23,355] [INFO] Task succeeded: fastANI
[2023-06-27 15:02:23,378] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:02:23,378] [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_013001885.1	s__JABDPF01 sp013001885	77.3695	181	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.83	99.83	0.95	0.93	4	-
GCA_013042915.1	s__JABDPF01 sp013042915	77.353	175	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.63	99.57	0.88	0.85	4	-
GCA_011773845.1	s__WVWV01 sp011773845	77.3083	135	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__WVWV01	95.0	100.00	100.00	0.99	0.98	6	-
GCF_008725655.1	s__W260 sp008725655	77.1889	133	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__W260	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003410055.1	s__Wenzhouxiangella sediminis	76.8076	68	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	76.3808	70	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002505.1	s__JABDJL01 sp013002505	76.3776	64	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761445.1	s__Oleiagrimonas soli	76.3465	66	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014842975.1	s__Rhodanobacter sp014842975	76.2756	64	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908385.1	s__Wenzhouxiangella sp009908385	76.2102	70	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524975.1	s__WTJD01 sp011524975	76.2049	82	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__WTJD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	76.1485	80	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	76.1446	78	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.1202	65	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997455.1	s__JAGOEZ01 sp017997455	76.1052	64	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JAGOEZ01	95.0	98.60	98.27	0.77	0.77	3	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	75.9537	61	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	75.9087	60	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	75.9061	58	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725155.1	s__Tahibacter sp001725155	75.85	81	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCF_004803715.2	s__Luteimonas yindakuii	75.8082	56	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.11	98.11	0.97	0.97	2	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	75.7393	52	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCA_003497545.1	s__Arenimonas sp003497545	75.3808	50	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-27 15:02:23,381] [INFO] GTDB search result was written to GCA_026193295.1_ASM2619329v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:02:23,381] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:02:23,386] [INFO] DFAST_QC result json was written to GCA_026193295.1_ASM2619329v1_genomic.fna/dqc_result.json
[2023-06-27 15:02:23,387] [INFO] DFAST_QC completed!
[2023-06-27 15:02:23,387] [INFO] Total running time: 0h1m16s