[2024-01-24 11:44:05,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference
[2024-01-24 11:44:08,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,839] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,839] [INFO] Running command: gunzip -c /var/lib/cwl/stgd115167b-dced-4702-9176-c79d8e98e329/GCF_017498525.1_ASM1749852v1_genomic.fna.gz | prodigal -d GCF_017498525.1_ASM1749852v1_genomic.fna/cds.fna -a GCF_017498525.1_ASM1749852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:24,687] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:24,687] [INFO] Task started: HMMsearch
[2024-01-24 11:44:24,687] [INFO] Running command: hmmsearch --tblout GCF_017498525.1_ASM1749852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/reference_markers.hmm GCF_017498525.1_ASM1749852v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:24,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:24,984] [INFO] Found 6/6 markers.
[2024-01-24 11:44:25,024] [INFO] Query marker FASTA was written to GCF_017498525.1_ASM1749852v1_genomic.fna/markers.fasta
[2024-01-24 11:44:25,025] [INFO] Task started: Blastn
[2024-01-24 11:44:25,025] [INFO] Running command: blastn -query GCF_017498525.1_ASM1749852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/reference_markers.fasta -out GCF_017498525.1_ASM1749852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:26,006] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:26,009] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:26,009] [INFO] Target genome list was writen to GCF_017498525.1_ASM1749852v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:26,028] [INFO] Task started: fastANI
[2024-01-24 11:44:26,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgd115167b-dced-4702-9176-c79d8e98e329/GCF_017498525.1_ASM1749852v1_genomic.fna.gz --refList GCF_017498525.1_ASM1749852v1_genomic.fna/target_genomes.txt --output GCF_017498525.1_ASM1749852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:45,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:45,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:45,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:45,341] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:45,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:45,342] [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
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	100.0	1438	1440	95	conclusive
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	85.3916	922	1440	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	82.1908	810	1440	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.3226	368	1440	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.0694	623	1440	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.839	563	1440	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.7936	607	1440	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	79.791	598	1440	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.6629	566	1440	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	79.6226	530	1440	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.5086	654	1440	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.4692	592	1440	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	79.4373	542	1440	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.3691	644	1440	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	79.2889	597	1440	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.1137	486	1440	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.009	620	1440	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	78.9301	540	1440	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	78.7404	492	1440	95	below_threshold
Ottowia thiooxydans	strain=DSM 14619	GCA_000422885.1	219182	219182	type	True	77.6999	417	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:45,344] [INFO] DFAST Taxonomy check result was written to GCF_017498525.1_ASM1749852v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:45,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:45,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:45,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/checkm_data
[2024-01-24 11:44:45,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:45,385] [INFO] Task started: CheckM
[2024-01-24 11:44:45,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498525.1_ASM1749852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498525.1_ASM1749852v1_genomic.fna/checkm_input GCF_017498525.1_ASM1749852v1_genomic.fna/checkm_result
[2024-01-24 11:45:43,170] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:43,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:43,191] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:43,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:43,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498525.1_ASM1749852v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:43,192] [INFO] Task started: Blastn
[2024-01-24 11:45:43,192] [INFO] Running command: blastn -query GCF_017498525.1_ASM1749852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07157fc4-6ca5-4797-a176-1351c1b2ae91/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498525.1_ASM1749852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:45,163] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:45,167] [INFO] Selected 13 target genomes.
[2024-01-24 11:45:45,167] [INFO] Target genome list was writen to GCF_017498525.1_ASM1749852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:45,181] [INFO] Task started: fastANI
[2024-01-24 11:45:45,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgd115167b-dced-4702-9176-c79d8e98e329/GCF_017498525.1_ASM1749852v1_genomic.fna.gz --refList GCF_017498525.1_ASM1749852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498525.1_ASM1749852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:57,868] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:57,894] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:57,894] [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_017498525.1	s__Ottowia sp017498525	100.0	1438	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018060485.1	s__Ottowia sp018060485	86.5147	633	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.99	98.80	0.82	0.79	7	-
GCA_013423955.1	s__Ottowia beijingensis	85.3777	923	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	97.71	97.71	0.88	0.88	2	-
GCA_016702555.1	s__Ottowia sp016702555	84.3862	820	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCA_001897615.1	s__Ottowia sp001897615	83.5857	747	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCA_016703145.1	s__Ottowia sp016703145	83.2957	770	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCA_017307865.1	s__Ottowia sp017307865	82.747	760	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCF_008017535.1	s__Ottowia sp008017535	82.3557	817	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008535.1	s__Ottowia oryzae	82.1926	809	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241325.1	s__Ottowia sp018241325	82.097	724	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997715.1	s__Ottowia sp017997715	82.0723	676	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015159745.1	s__Ramlibacter aquaticus	79.6313	569	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	-
GCA_018242005.1	s__Alicycliphilus sp018242005	79.5856	513	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:57,896] [INFO] GTDB search result was written to GCF_017498525.1_ASM1749852v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:57,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:57,901] [INFO] DFAST_QC result json was written to GCF_017498525.1_ASM1749852v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:57,902] [INFO] DFAST_QC completed!
[2024-01-24 11:45:57,902] [INFO] Total running time: 0h1m52s