[2024-01-24 12:42:09,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference
[2024-01-24 12:42:10,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,848] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,848] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf9d370f-5a4d-4a8a-b029-6a476a09238b/GCF_011764585.1_ASM1176458v1_genomic.fna.gz | prodigal -d GCF_011764585.1_ASM1176458v1_genomic.fna/cds.fna -a GCF_011764585.1_ASM1176458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:23,346] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:23,347] [INFO] Task started: HMMsearch
[2024-01-24 12:42:23,347] [INFO] Running command: hmmsearch --tblout GCF_011764585.1_ASM1176458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/reference_markers.hmm GCF_011764585.1_ASM1176458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:23,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:23,627] [INFO] Found 6/6 markers.
[2024-01-24 12:42:23,665] [INFO] Query marker FASTA was written to GCF_011764585.1_ASM1176458v1_genomic.fna/markers.fasta
[2024-01-24 12:42:23,665] [INFO] Task started: Blastn
[2024-01-24 12:42:23,666] [INFO] Running command: blastn -query GCF_011764585.1_ASM1176458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/reference_markers.fasta -out GCF_011764585.1_ASM1176458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:24,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:24,647] [INFO] Selected 26 target genomes.
[2024-01-24 12:42:24,647] [INFO] Target genome list was writen to GCF_011764585.1_ASM1176458v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:24,658] [INFO] Task started: fastANI
[2024-01-24 12:42:24,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf9d370f-5a4d-4a8a-b029-6a476a09238b/GCF_011764585.1_ASM1176458v1_genomic.fna.gz --refList GCF_011764585.1_ASM1176458v1_genomic.fna/target_genomes.txt --output GCF_011764585.1_ASM1176458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:42,682] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:42,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:42,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:42,703] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:42:42,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:42,703] [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
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	100.0	1274	1275	95	conclusive
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	79.2085	362	1275	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	78.09	207	1275	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.9867	231	1275	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.9197	254	1275	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.8962	267	1275	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.7774	204	1275	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	77.3977	214	1275	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	77.2516	203	1275	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	77.2274	193	1275	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	77.2103	189	1275	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.1222	208	1275	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	77.1063	140	1275	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	77.0992	151	1275	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.9623	142	1275	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	76.8435	225	1275	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	76.8314	187	1275	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	76.8053	227	1275	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.7825	168	1275	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	76.7818	111	1275	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	76.6021	190	1275	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.4584	178	1275	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.0992	103	1275	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	75.5411	106	1275	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.5044	106	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:42,705] [INFO] DFAST Taxonomy check result was written to GCF_011764585.1_ASM1176458v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:42,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:42,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:42,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/checkm_data
[2024-01-24 12:42:42,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:42,749] [INFO] Task started: CheckM
[2024-01-24 12:42:42,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011764585.1_ASM1176458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011764585.1_ASM1176458v1_genomic.fna/checkm_input GCF_011764585.1_ASM1176458v1_genomic.fna/checkm_result
[2024-01-24 12:43:21,449] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:21,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:21,474] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:21,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:21,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011764585.1_ASM1176458v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:21,476] [INFO] Task started: Blastn
[2024-01-24 12:43:21,476] [INFO] Running command: blastn -query GCF_011764585.1_ASM1176458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85f578c4-960e-4716-92e2-45b7193c7461/dqc_reference/reference_markers_gtdb.fasta -out GCF_011764585.1_ASM1176458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:23,409] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:23,413] [INFO] Selected 15 target genomes.
[2024-01-24 12:43:23,413] [INFO] Target genome list was writen to GCF_011764585.1_ASM1176458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:23,427] [INFO] Task started: fastANI
[2024-01-24 12:43:23,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf9d370f-5a4d-4a8a-b029-6a476a09238b/GCF_011764585.1_ASM1176458v1_genomic.fna.gz --refList GCF_011764585.1_ASM1176458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011764585.1_ASM1176458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:32,363] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:32,383] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:32,383] [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_011764585.1	s__Sulfurimicrobium lacus	100.0	1273	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003104895.1	s__Sulfurimicrobium sp003104895	81.7024	477	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002632355.1	s__Sulfurimicrobium denitrificans_A	80.6606	511	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018824405.1	s__Sulfurimicrobium sp018824405	80.2246	537	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002784065.1	s__Sulfuricella sp002784065	79.1627	329	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	99.65	99.21	0.84	0.80	4	-
GCA_018823025.1	s__Sulfuricella sp018823025	78.477	316	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	99.85	99.85	0.92	0.92	2	-
GCA_018336195.1	s__JAGXQV01 sp018336195	78.3063	377	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__JAGXQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183575.1	s__Gallionella sp016183575	77.4997	143	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730115.1	s__Pseudomethylobacillus aquaticus	77.0868	141	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235775.1	s__RBG-16-58-11 sp016235775	76.9434	199	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__RBG-16-58-11;g__RBG-16-58-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	76.8339	226	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001801055.1	s__Gallionella sp001801055	76.766	100	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.4289	85	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.0837	104	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885165.1	s__Gallionella sp903885165	76.0099	59	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	99.76	99.35	0.93	0.83	60	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:32,386] [INFO] GTDB search result was written to GCF_011764585.1_ASM1176458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:32,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:32,390] [INFO] DFAST_QC result json was written to GCF_011764585.1_ASM1176458v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:32,390] [INFO] DFAST_QC completed!
[2024-01-24 12:43:32,390] [INFO] Total running time: 0h1m23s