[2023-06-17 10:34:06,573] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:34:06,591] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:34:06,591] [INFO] DQC Reference Directory: /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference
[2023-06-17 10:34:08,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:34:08,163] [INFO] Task started: Prodigal
[2023-06-17 10:34:08,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg27cb0805-112c-4592-8336-dc2215cf4ad1/GCA_009920175.1_ASM992017v1_genomic.fna.gz | prodigal -d GCA_009920175.1_ASM992017v1_genomic.fna/cds.fna -a GCA_009920175.1_ASM992017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:34:17,789] [INFO] Task succeeded: Prodigal
[2023-06-17 10:34:17,789] [INFO] Task started: HMMsearch
[2023-06-17 10:34:17,789] [INFO] Running command: hmmsearch --tblout GCA_009920175.1_ASM992017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/reference_markers.hmm GCA_009920175.1_ASM992017v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:34:18,081] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:34:18,082] [INFO] Found 6/6 markers.
[2023-06-17 10:34:18,114] [INFO] Query marker FASTA was written to GCA_009920175.1_ASM992017v1_genomic.fna/markers.fasta
[2023-06-17 10:34:18,115] [INFO] Task started: Blastn
[2023-06-17 10:34:18,115] [INFO] Running command: blastn -query GCA_009920175.1_ASM992017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/reference_markers.fasta -out GCA_009920175.1_ASM992017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:34:18,820] [INFO] Task succeeded: Blastn
[2023-06-17 10:34:18,829] [INFO] Selected 23 target genomes.
[2023-06-17 10:34:18,829] [INFO] Target genome list was writen to GCA_009920175.1_ASM992017v1_genomic.fna/target_genomes.txt
[2023-06-17 10:34:18,854] [INFO] Task started: fastANI
[2023-06-17 10:34:18,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cb0805-112c-4592-8336-dc2215cf4ad1/GCA_009920175.1_ASM992017v1_genomic.fna.gz --refList GCA_009920175.1_ASM992017v1_genomic.fna/target_genomes.txt --output GCA_009920175.1_ASM992017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:34:35,249] [INFO] Task succeeded: fastANI
[2023-06-17 10:34:35,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:34:35,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:34:35,271] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 10:34:35,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 10:34:35,272] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	78.0836	167	658	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.807	184	658	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.7953	191	658	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.5176	103	658	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.273	157	658	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	76.9607	76	658	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.8571	105	658	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.8427	102	658	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.8397	100	658	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.8309	102	658	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.817	88	658	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.7056	108	658	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.6891	110	658	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.5393	79	658	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	76.3974	70	658	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	76.3734	67	658	95	below_threshold
Ottowia thiooxydans	strain=DSM 14619	GCA_000422885.1	219182	219182	type	True	76.3242	59	658	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	76.3197	86	658	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.1812	65	658	95	below_threshold
Brachymonas chironomi	strain=DSM 19884	GCA_000374625.1	491919	491919	type	True	76.0196	50	658	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 10:34:35,277] [INFO] DFAST Taxonomy check result was written to GCA_009920175.1_ASM992017v1_genomic.fna/tc_result.tsv
[2023-06-17 10:34:35,278] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:34:35,278] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:34:35,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/checkm_data
[2023-06-17 10:34:35,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:34:35,313] [INFO] Task started: CheckM
[2023-06-17 10:34:35,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009920175.1_ASM992017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009920175.1_ASM992017v1_genomic.fna/checkm_input GCA_009920175.1_ASM992017v1_genomic.fna/checkm_result
[2023-06-17 10:35:10,349] [INFO] Task succeeded: CheckM
[2023-06-17 10:35:10,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.59%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 10:35:10,375] [INFO] ===== Completeness check finished =====
[2023-06-17 10:35:10,375] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:35:10,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009920175.1_ASM992017v1_genomic.fna/markers.fasta)
[2023-06-17 10:35:10,376] [INFO] Task started: Blastn
[2023-06-17 10:35:10,376] [INFO] Running command: blastn -query GCA_009920175.1_ASM992017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0263d80-afda-4c0b-aba5-9eaa5bdeae56/dqc_reference/reference_markers_gtdb.fasta -out GCA_009920175.1_ASM992017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:35:11,496] [INFO] Task succeeded: Blastn
[2023-06-17 10:35:11,500] [INFO] Selected 12 target genomes.
[2023-06-17 10:35:11,500] [INFO] Target genome list was writen to GCA_009920175.1_ASM992017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:35:11,516] [INFO] Task started: fastANI
[2023-06-17 10:35:11,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cb0805-112c-4592-8336-dc2215cf4ad1/GCA_009920175.1_ASM992017v1_genomic.fna.gz --refList GCA_009920175.1_ASM992017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009920175.1_ASM992017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:35:18,830] [INFO] Task succeeded: fastANI
[2023-06-17 10:35:18,846] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:35:18,846] [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_009928125.1	s__Limnohabitans_A sp009928125	99.1265	507	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.84	98.65	0.83	0.81	5	conclusive
GCF_001412575.1	s__Limnohabitans_A sp001412575	89.5124	572	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	82.1432	412	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063375.1	s__Limnohabitans_A sp003063375	81.1102	373	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693505.1	s__Limnohabitans_A sp009693505	80.6478	380	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	80.4163	264	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	80.0993	342	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCA_005789685.1	s__Limnohabitans_A sp005789685	80.0745	250	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916355.1	s__Limnohabitans_A sp903916355	78.0022	196	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	77.5334	207	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.0317	116	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCF_000381265.1	s__Curvibacter lanceolatus	76.8397	100	658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-17 10:35:18,849] [INFO] GTDB search result was written to GCA_009920175.1_ASM992017v1_genomic.fna/result_gtdb.tsv
[2023-06-17 10:35:18,850] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:35:18,855] [INFO] DFAST_QC result json was written to GCA_009920175.1_ASM992017v1_genomic.fna/dqc_result.json
[2023-06-17 10:35:18,855] [INFO] DFAST_QC completed!
[2023-06-17 10:35:18,855] [INFO] Total running time: 0h1m12s