[2024-01-24 15:01:23,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,326] [INFO] DQC Reference Directory: /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference
[2024-01-24 15:01:24,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,722] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg24326dd9-420b-4bfe-b325-0829b357e229/GCF_004366735.1_ASM436673v1_genomic.fna.gz | prodigal -d GCF_004366735.1_ASM436673v1_genomic.fna/cds.fna -a GCF_004366735.1_ASM436673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:33,711] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:33,712] [INFO] Task started: HMMsearch
[2024-01-24 15:01:33,712] [INFO] Running command: hmmsearch --tblout GCF_004366735.1_ASM436673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/reference_markers.hmm GCF_004366735.1_ASM436673v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:34,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:34,013] [INFO] Found 6/6 markers.
[2024-01-24 15:01:34,042] [INFO] Query marker FASTA was written to GCF_004366735.1_ASM436673v1_genomic.fna/markers.fasta
[2024-01-24 15:01:34,043] [INFO] Task started: Blastn
[2024-01-24 15:01:34,043] [INFO] Running command: blastn -query GCF_004366735.1_ASM436673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/reference_markers.fasta -out GCF_004366735.1_ASM436673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:35,001] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:35,006] [INFO] Selected 26 target genomes.
[2024-01-24 15:01:35,006] [INFO] Target genome list was writen to GCF_004366735.1_ASM436673v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:35,022] [INFO] Task started: fastANI
[2024-01-24 15:01:35,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg24326dd9-420b-4bfe-b325-0829b357e229/GCF_004366735.1_ASM436673v1_genomic.fna.gz --refList GCF_004366735.1_ASM436673v1_genomic.fna/target_genomes.txt --output GCF_004366735.1_ASM436673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:52,140] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:52,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:52,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:52,163] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:52,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:52,163] [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
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	100.0	961	963	95	conclusive
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.4984	245	963	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	77.2248	91	963	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.1986	194	963	95	below_threshold
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	77.021	64	963	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	77.0066	96	963	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.9489	173	963	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	76.9056	79	963	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.7729	154	963	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.6739	97	963	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	76.6149	108	963	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.5498	105	963	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.5358	92	963	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	76.5317	97	963	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	76.3172	59	963	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	76.1513	55	963	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.0774	96	963	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	76.0688	80	963	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.967	92	963	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.94	97	963	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	75.7253	59	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:52,165] [INFO] DFAST Taxonomy check result was written to GCF_004366735.1_ASM436673v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:52,166] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:52,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:52,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/checkm_data
[2024-01-24 15:01:52,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:52,206] [INFO] Task started: CheckM
[2024-01-24 15:01:52,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366735.1_ASM436673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366735.1_ASM436673v1_genomic.fna/checkm_input GCF_004366735.1_ASM436673v1_genomic.fna/checkm_result
[2024-01-24 15:02:22,123] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:22,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:22,146] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:22,146] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:22,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366735.1_ASM436673v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:22,147] [INFO] Task started: Blastn
[2024-01-24 15:02:22,147] [INFO] Running command: blastn -query GCF_004366735.1_ASM436673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a01dcc-cf35-472d-b802-af9c90619a16/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366735.1_ASM436673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:23,665] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:23,670] [INFO] Selected 26 target genomes.
[2024-01-24 15:02:23,670] [INFO] Target genome list was writen to GCF_004366735.1_ASM436673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:23,735] [INFO] Task started: fastANI
[2024-01-24 15:02:23,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg24326dd9-420b-4bfe-b325-0829b357e229/GCF_004366735.1_ASM436673v1_genomic.fna.gz --refList GCF_004366735.1_ASM436673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366735.1_ASM436673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:39,105] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:39,126] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:39,126] [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_004366735.1	s__Thiohalophilus thiocyanatoxydans	100.0	961	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__Thiohalophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.5919	241	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.562	155	963	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	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	77.4984	245	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051615.1	s__HyVt-448 sp011051615	77.2402	146	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__HyVt-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	77.2187	112	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_002699185.1	s__Thiohalobacter sp002699185	77.2128	183	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	77.1986	194	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	77.1944	207	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	77.004	131	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051685.1	s__SZUA-152 sp011051685	76.9913	122	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.9241	138	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.78	118	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.7729	154	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	76.7606	99	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002549795.1	s__Halomonas beimenensis	76.7384	98	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491815.1	s__JAADGZ01 sp015491815	76.6947	128	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__JAADGZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	76.6149	108	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	76.6023	99	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	76.5403	100	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCA_018435665.1	s__M0108 sp018435665	76.5272	83	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCF_017309075.1	s__Motiliproteus sp017309075	76.4138	67	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464965.1	s__Ga0077554 sp001464965	76.4032	71	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077554;f__Ga007554;g__Ga0077554	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:39,128] [INFO] GTDB search result was written to GCF_004366735.1_ASM436673v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:39,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:39,133] [INFO] DFAST_QC result json was written to GCF_004366735.1_ASM436673v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:39,133] [INFO] DFAST_QC completed!
[2024-01-24 15:02:39,134] [INFO] Total running time: 0h1m16s