[2024-01-24 12:22:37,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference
[2024-01-24 12:22:39,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,152] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,152] [INFO] Running command: gunzip -c /var/lib/cwl/stga76d56a5-fc21-4cd1-95e0-8e95c5e0cd15/GCF_001463945.1_ASM146394v1_genomic.fna.gz | prodigal -d GCF_001463945.1_ASM146394v1_genomic.fna/cds.fna -a GCF_001463945.1_ASM146394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:52,611] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:52,611] [INFO] Task started: HMMsearch
[2024-01-24 12:22:52,611] [INFO] Running command: hmmsearch --tblout GCF_001463945.1_ASM146394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/reference_markers.hmm GCF_001463945.1_ASM146394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:52,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:52,902] [INFO] Found 6/6 markers.
[2024-01-24 12:22:52,947] [INFO] Query marker FASTA was written to GCF_001463945.1_ASM146394v1_genomic.fna/markers.fasta
[2024-01-24 12:22:52,947] [INFO] Task started: Blastn
[2024-01-24 12:22:52,948] [INFO] Running command: blastn -query GCF_001463945.1_ASM146394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/reference_markers.fasta -out GCF_001463945.1_ASM146394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,035] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,039] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:54,040] [INFO] Target genome list was writen to GCF_001463945.1_ASM146394v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:54,045] [INFO] Task started: fastANI
[2024-01-24 12:22:54,046] [INFO] Running command: fastANI --query /var/lib/cwl/stga76d56a5-fc21-4cd1-95e0-8e95c5e0cd15/GCF_001463945.1_ASM146394v1_genomic.fna.gz --refList GCF_001463945.1_ASM146394v1_genomic.fna/target_genomes.txt --output GCF_001463945.1_ASM146394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:06,936] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:06,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:06,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:06,953] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:06,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:06,953] [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
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	100.0	1649	1652	95	conclusive
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	99.994	1644	1652	95	conclusive
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	82.1334	839	1652	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	81.9207	916	1652	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	81.8941	847	1652	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	80.9867	782	1652	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	80.1314	586	1652	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.16	570	1652	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	78.9233	592	1652	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.586	433	1652	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.444	330	1652	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.4423	330	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,955] [INFO] DFAST Taxonomy check result was written to GCF_001463945.1_ASM146394v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:06,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:06,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:06,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/checkm_data
[2024-01-24 12:23:06,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:07,007] [INFO] Task started: CheckM
[2024-01-24 12:23:07,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001463945.1_ASM146394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001463945.1_ASM146394v1_genomic.fna/checkm_input GCF_001463945.1_ASM146394v1_genomic.fna/checkm_result
[2024-01-24 12:23:49,032] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:49,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:49,059] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:49,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:49,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001463945.1_ASM146394v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:49,060] [INFO] Task started: Blastn
[2024-01-24 12:23:49,060] [INFO] Running command: blastn -query GCF_001463945.1_ASM146394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2767da9e-4cbb-4f93-85c6-3b4a09ecc632/dqc_reference/reference_markers_gtdb.fasta -out GCF_001463945.1_ASM146394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:51,206] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:51,211] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:51,212] [INFO] Target genome list was writen to GCF_001463945.1_ASM146394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:51,234] [INFO] Task started: fastANI
[2024-01-24 12:23:51,235] [INFO] Running command: fastANI --query /var/lib/cwl/stga76d56a5-fc21-4cd1-95e0-8e95c5e0cd15/GCF_001463945.1_ASM146394v1_genomic.fna.gz --refList GCF_001463945.1_ASM146394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001463945.1_ASM146394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:02,668] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:02,681] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:02,681] [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_000382705.1	s__Aureimonas ureilytica	99.994	1644	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001475935.1	s__Aureimonas ureilytica_A	86.0486	1047	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	96.93	96.78	0.87	0.86	4	-
GCF_001442755.1	s__Aureimonas sp001442755	86.048	1143	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	98.47	96.94	0.96	0.92	3	-
GCF_001423245.1	s__Aureimonas sp001423245	82.2319	833	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	82.0154	897	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463745.1	s__Aureimonas sp001463745	81.9555	801	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583935.1	s__Aureimonas flava	81.912	844	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	81.9118	915	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463765.1	s__Aureimonas sp001463765	81.4363	795	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104035.1	s__Aureimonas jatrophae	81.0084	771	1652	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:02,683] [INFO] GTDB search result was written to GCF_001463945.1_ASM146394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:02,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:02,687] [INFO] DFAST_QC result json was written to GCF_001463945.1_ASM146394v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:02,688] [INFO] DFAST_QC completed!
[2024-01-24 12:24:02,688] [INFO] Total running time: 0h1m25s