[2023-06-28 04:37:19,324] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:19,327] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:19,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference
[2023-06-28 04:37:20,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:20,558] [INFO] Task started: Prodigal
[2023-06-28 04:37:20,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa10b340-1dfd-4891-a77d-666643fa8ed7/GCA_913773955.1_S2C41209_SP48_genomic.fna.gz | prodigal -d GCA_913773955.1_S2C41209_SP48_genomic.fna/cds.fna -a GCA_913773955.1_S2C41209_SP48_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:30,954] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:30,955] [INFO] Task started: HMMsearch
[2023-06-28 04:37:30,955] [INFO] Running command: hmmsearch --tblout GCA_913773955.1_S2C41209_SP48_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/reference_markers.hmm GCA_913773955.1_S2C41209_SP48_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:31,250] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:31,251] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfa10b340-1dfd-4891-a77d-666643fa8ed7/GCA_913773955.1_S2C41209_SP48_genomic.fna.gz]
[2023-06-28 04:37:31,281] [INFO] Query marker FASTA was written to GCA_913773955.1_S2C41209_SP48_genomic.fna/markers.fasta
[2023-06-28 04:37:31,281] [INFO] Task started: Blastn
[2023-06-28 04:37:31,282] [INFO] Running command: blastn -query GCA_913773955.1_S2C41209_SP48_genomic.fna/markers.fasta -db /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/reference_markers.fasta -out GCA_913773955.1_S2C41209_SP48_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:32,059] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:32,063] [INFO] Selected 13 target genomes.
[2023-06-28 04:37:32,064] [INFO] Target genome list was writen to GCA_913773955.1_S2C41209_SP48_genomic.fna/target_genomes.txt
[2023-06-28 04:37:32,065] [INFO] Task started: fastANI
[2023-06-28 04:37:32,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa10b340-1dfd-4891-a77d-666643fa8ed7/GCA_913773955.1_S2C41209_SP48_genomic.fna.gz --refList GCA_913773955.1_S2C41209_SP48_genomic.fna/target_genomes.txt --output GCA_913773955.1_S2C41209_SP48_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:46,888] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:46,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:46,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:46,900] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 04:37:46,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 04:37:46,900] [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
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	96.8926	1001	1104	95	conclusive
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	84.6431	812	1104	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	84.6169	820	1104	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	84.4743	744	1104	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	84.4289	793	1104	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	84.2276	764	1104	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	83.5859	750	1104	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	83.2631	734	1104	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3433	550	1104	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2987	544	1104	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8182	564	1104	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.7147	589	1104	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.513	495	1104	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:37:46,903] [INFO] DFAST Taxonomy check result was written to GCA_913773955.1_S2C41209_SP48_genomic.fna/tc_result.tsv
[2023-06-28 04:37:46,904] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:46,904] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:46,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/checkm_data
[2023-06-28 04:37:46,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:46,946] [INFO] Task started: CheckM
[2023-06-28 04:37:46,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913773955.1_S2C41209_SP48_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913773955.1_S2C41209_SP48_genomic.fna/checkm_input GCA_913773955.1_S2C41209_SP48_genomic.fna/checkm_result
[2023-06-28 04:38:25,527] [INFO] Task succeeded: CheckM
[2023-06-28 04:38:25,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:38:25,550] [INFO] ===== Completeness check finished =====
[2023-06-28 04:38:25,550] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:38:25,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913773955.1_S2C41209_SP48_genomic.fna/markers.fasta)
[2023-06-28 04:38:25,551] [INFO] Task started: Blastn
[2023-06-28 04:38:25,551] [INFO] Running command: blastn -query GCA_913773955.1_S2C41209_SP48_genomic.fna/markers.fasta -db /var/lib/cwl/stg46007757-78f9-4bd0-b87e-519b99d5fef3/dqc_reference/reference_markers_gtdb.fasta -out GCA_913773955.1_S2C41209_SP48_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:38:26,803] [INFO] Task succeeded: Blastn
[2023-06-28 04:38:26,808] [INFO] Selected 10 target genomes.
[2023-06-28 04:38:26,808] [INFO] Target genome list was writen to GCA_913773955.1_S2C41209_SP48_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:38:26,811] [INFO] Task started: fastANI
[2023-06-28 04:38:26,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa10b340-1dfd-4891-a77d-666643fa8ed7/GCA_913773955.1_S2C41209_SP48_genomic.fna.gz --refList GCA_913773955.1_S2C41209_SP48_genomic.fna/target_genomes_gtdb.txt --output GCA_913773955.1_S2C41209_SP48_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:38:38,391] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:38,403] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:38:38,403] [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_900113035.1	s__Acidovorax_A wautersii	96.8926	1001	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424265.1	s__Acidovorax_A sp001424265	86.9306	837	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	84.7059	776	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687165.1	s__Acidovorax_A oryzae	84.6002	816	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_003269065.1	s__Acidovorax_A anthurii	84.4339	747	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	84.2269	764	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_900112675.1	s__Acidovorax_A konjaci	83.5835	749	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102625.1	s__Acidovorax_A valerianellae	83.2181	737	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	83.1535	706	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_003053545.1	s__Acidovorax sp003053545	82.5552	758	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-28 04:38:38,406] [INFO] GTDB search result was written to GCA_913773955.1_S2C41209_SP48_genomic.fna/result_gtdb.tsv
[2023-06-28 04:38:38,406] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:38:38,410] [INFO] DFAST_QC result json was written to GCA_913773955.1_S2C41209_SP48_genomic.fna/dqc_result.json
[2023-06-28 04:38:38,410] [INFO] DFAST_QC completed!
[2023-06-28 04:38:38,410] [INFO] Total running time: 0h1m19s