[2024-01-24 12:23:51,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:51,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:51,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference
[2024-01-24 12:23:52,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,426] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg7777d9db-0d07-4b67-b805-21ae3f71879d/GCF_016653115.1_ASM1665311v1_genomic.fna.gz | prodigal -d GCF_016653115.1_ASM1665311v1_genomic.fna/cds.fna -a GCF_016653115.1_ASM1665311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:02,288] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:02,289] [INFO] Task started: HMMsearch
[2024-01-24 12:24:02,289] [INFO] Running command: hmmsearch --tblout GCF_016653115.1_ASM1665311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/reference_markers.hmm GCF_016653115.1_ASM1665311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:02,574] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:02,576] [INFO] Found 6/6 markers.
[2024-01-24 12:24:02,615] [INFO] Query marker FASTA was written to GCF_016653115.1_ASM1665311v1_genomic.fna/markers.fasta
[2024-01-24 12:24:02,615] [INFO] Task started: Blastn
[2024-01-24 12:24:02,616] [INFO] Running command: blastn -query GCF_016653115.1_ASM1665311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/reference_markers.fasta -out GCF_016653115.1_ASM1665311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,669] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,672] [INFO] Selected 12 target genomes.
[2024-01-24 12:24:03,673] [INFO] Target genome list was writen to GCF_016653115.1_ASM1665311v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:03,679] [INFO] Task started: fastANI
[2024-01-24 12:24:03,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg7777d9db-0d07-4b67-b805-21ae3f71879d/GCF_016653115.1_ASM1665311v1_genomic.fna.gz --refList GCF_016653115.1_ASM1665311v1_genomic.fna/target_genomes.txt --output GCF_016653115.1_ASM1665311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:14,677] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:14,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:14,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:14,694] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:14,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:14,695] [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
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	100.0	1167	1170	95	conclusive
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	83.2149	626	1170	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	83.2058	632	1170	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	81.4282	485	1170	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	80.0026	456	1170	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.9408	395	1170	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	78.9009	283	1170	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.7415	361	1170	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.6849	338	1170	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	77.2616	325	1170	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.2399	375	1170	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	77.113	306	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:14,696] [INFO] DFAST Taxonomy check result was written to GCF_016653115.1_ASM1665311v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:14,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:14,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:14,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/checkm_data
[2024-01-24 12:24:14,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:14,735] [INFO] Task started: CheckM
[2024-01-24 12:24:14,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653115.1_ASM1665311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653115.1_ASM1665311v1_genomic.fna/checkm_input GCF_016653115.1_ASM1665311v1_genomic.fna/checkm_result
[2024-01-24 12:24:47,107] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:47,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:47,129] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:47,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:47,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653115.1_ASM1665311v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:47,130] [INFO] Task started: Blastn
[2024-01-24 12:24:47,130] [INFO] Running command: blastn -query GCF_016653115.1_ASM1665311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5673d3ee-70af-43a8-85d6-e54d375847a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653115.1_ASM1665311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:49,264] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:49,269] [INFO] Selected 14 target genomes.
[2024-01-24 12:24:49,270] [INFO] Target genome list was writen to GCF_016653115.1_ASM1665311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:49,280] [INFO] Task started: fastANI
[2024-01-24 12:24:49,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg7777d9db-0d07-4b67-b805-21ae3f71879d/GCF_016653115.1_ASM1665311v1_genomic.fna.gz --refList GCF_016653115.1_ASM1665311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653115.1_ASM1665311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:01,754] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:01,781] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:01,782] [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_016653115.1	s__Rhodocyclus purpureus	100.0	1167	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014197755.1	s__Rhodocyclus tenuis	83.243	629	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	-
GCA_001897745.1	s__66-26 sp001897745	81.5207	553	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
GCF_016858125.1	s__Azospira_A restricta	81.5086	556	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011881425.1	s__Rhodocyclus tenuis_A	81.3908	480	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.99	98.97	0.94	0.93	3	-
GCA_016183655.1	s__Azospira_A sp016183655	81.0228	509	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469585.1	s__Azonexus sp009469585	79.4655	414	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262095.1	s__Propionivibrio sp018262095	79.4237	423	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208425.1	s__JACQYA01 sp016208425	79.2974	379	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995515.1	s__Propionivibrio sp017995515	79.2869	374	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017592775.1	s__Accumulibacter sp017592775	78.945	401	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.29	99.29	0.85	0.85	2	-
GCF_000687455.2	s__Burkholderia sp000687455	77.3145	284	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343775.1	s__Burkholderia sp004343775	77.2318	349	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899425.1	s__Burkholderia sp002223185	77.0861	325	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.86	95.32	0.94	0.84	68	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:01,813] [INFO] GTDB search result was written to GCF_016653115.1_ASM1665311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:01,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:01,820] [INFO] DFAST_QC result json was written to GCF_016653115.1_ASM1665311v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:01,820] [INFO] DFAST_QC completed!
[2024-01-24 12:25:01,820] [INFO] Total running time: 0h1m11s