[2024-01-24 14:12:59,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:59,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:59,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference
[2024-01-24 14:13:00,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:00,751] [INFO] Task started: Prodigal
[2024-01-24 14:13:00,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg848b8330-fbba-40d3-acf6-8b119d818b96/GCF_009617575.1_ASM961757v1_genomic.fna.gz | prodigal -d GCF_009617575.1_ASM961757v1_genomic.fna/cds.fna -a GCF_009617575.1_ASM961757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:09,308] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:09,308] [INFO] Task started: HMMsearch
[2024-01-24 14:13:09,309] [INFO] Running command: hmmsearch --tblout GCF_009617575.1_ASM961757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/reference_markers.hmm GCF_009617575.1_ASM961757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:09,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:09,550] [INFO] Found 6/6 markers.
[2024-01-24 14:13:09,583] [INFO] Query marker FASTA was written to GCF_009617575.1_ASM961757v1_genomic.fna/markers.fasta
[2024-01-24 14:13:09,583] [INFO] Task started: Blastn
[2024-01-24 14:13:09,583] [INFO] Running command: blastn -query GCF_009617575.1_ASM961757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/reference_markers.fasta -out GCF_009617575.1_ASM961757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:10,416] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:10,420] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:10,421] [INFO] Target genome list was writen to GCF_009617575.1_ASM961757v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:10,446] [INFO] Task started: fastANI
[2024-01-24 14:13:10,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg848b8330-fbba-40d3-acf6-8b119d818b96/GCF_009617575.1_ASM961757v1_genomic.fna.gz --refList GCF_009617575.1_ASM961757v1_genomic.fna/target_genomes.txt --output GCF_009617575.1_ASM961757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:19,992] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:19,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:20,007] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:20,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:20,007] [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 gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	100.0	965	965	95	conclusive
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	83.4082	653	965	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	83.3246	661	965	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	81.488	469	965	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	78.8485	249	965	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.6299	281	965	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.1536	283	965	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	76.8037	167	965	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	76.7098	191	965	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	75.7721	66	965	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	75.6936	73	965	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	74.9987	73	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,012] [INFO] DFAST Taxonomy check result was written to GCF_009617575.1_ASM961757v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:20,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:20,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:20,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/checkm_data
[2024-01-24 14:13:20,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:20,065] [INFO] Task started: CheckM
[2024-01-24 14:13:20,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009617575.1_ASM961757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009617575.1_ASM961757v1_genomic.fna/checkm_input GCF_009617575.1_ASM961757v1_genomic.fna/checkm_result
[2024-01-24 14:13:51,108] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:51,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:51,122] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:51,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:51,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009617575.1_ASM961757v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:51,123] [INFO] Task started: Blastn
[2024-01-24 14:13:51,123] [INFO] Running command: blastn -query GCF_009617575.1_ASM961757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a9de093-6dfd-4e04-9eb3-27af38a78425/dqc_reference/reference_markers_gtdb.fasta -out GCF_009617575.1_ASM961757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:52,652] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:52,655] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:52,655] [INFO] Target genome list was writen to GCF_009617575.1_ASM961757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:52,686] [INFO] Task started: fastANI
[2024-01-24 14:13:52,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg848b8330-fbba-40d3-acf6-8b119d818b96/GCF_009617575.1_ASM961757v1_genomic.fna.gz --refList GCF_009617575.1_ASM961757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009617575.1_ASM961757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:02,606] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:02,620] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:02,620] [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_011881425.1	s__Rhodocyclus tenuis_A	99.0096	899	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.99	98.97	0.94	0.93	3	conclusive
GCF_014197755.1	s__Rhodocyclus tenuis	83.4221	651	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	-
GCF_016653115.1	s__Rhodocyclus purpureus	81.4784	470	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897745.1	s__66-26 sp001897745	80.3363	479	965	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	79.7038	418	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183655.1	s__Azospira_A sp016183655	79.449	400	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995515.1	s__Propionivibrio sp017995515	78.9641	282	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262095.1	s__Propionivibrio sp018262095	78.9198	346	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	78.6466	283	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208425.1	s__JACQYA01 sp016208425	78.5731	327	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	78.4082	281	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	78.0085	273	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
GCA_016791205.1	s__Desulfobacillus sp016791205	77.7928	208	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000585055.1	s__Accumulibacter sp000585055	77.6074	235	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.81	99.81	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:02,623] [INFO] GTDB search result was written to GCF_009617575.1_ASM961757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:02,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:02,630] [INFO] DFAST_QC result json was written to GCF_009617575.1_ASM961757v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:02,630] [INFO] DFAST_QC completed!
[2024-01-24 14:14:02,630] [INFO] Total running time: 0h1m3s