[2024-01-24 13:57:55,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference
[2024-01-24 13:57:56,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,749] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgc68b1473-d6de-418a-bff2-60ab86e3a9df/GCF_013363755.1_ASM1336375v1_genomic.fna.gz | prodigal -d GCF_013363755.1_ASM1336375v1_genomic.fna/cds.fna -a GCF_013363755.1_ASM1336375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:20,545] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:20,546] [INFO] Task started: HMMsearch
[2024-01-24 13:58:20,546] [INFO] Running command: hmmsearch --tblout GCF_013363755.1_ASM1336375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/reference_markers.hmm GCF_013363755.1_ASM1336375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:20,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:20,861] [INFO] Found 6/6 markers.
[2024-01-24 13:58:20,909] [INFO] Query marker FASTA was written to GCF_013363755.1_ASM1336375v1_genomic.fna/markers.fasta
[2024-01-24 13:58:20,909] [INFO] Task started: Blastn
[2024-01-24 13:58:20,909] [INFO] Running command: blastn -query GCF_013363755.1_ASM1336375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/reference_markers.fasta -out GCF_013363755.1_ASM1336375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,065] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:22,066] [INFO] Target genome list was writen to GCF_013363755.1_ASM1336375v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:22,084] [INFO] Task started: fastANI
[2024-01-24 13:58:22,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68b1473-d6de-418a-bff2-60ab86e3a9df/GCF_013363755.1_ASM1336375v1_genomic.fna.gz --refList GCF_013363755.1_ASM1336375v1_genomic.fna/target_genomes.txt --output GCF_013363755.1_ASM1336375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:45,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:45,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:45,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:45,039] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:45,040] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:45,040] [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
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.0373	837	1674	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.983	946	1674	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.9497	759	1674	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.8713	920	1674	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.691	792	1674	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	81.0872	656	1674	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.6729	663	1674	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.6716	691	1674	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.6429	635	1674	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.6309	632	1674	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	80.5128	672	1674	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	80.2911	667	1674	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.2194	671	1674	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	80.1948	750	1674	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	80.1623	624	1674	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.097	661	1674	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.0209	721	1674	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.6894	599	1674	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.3683	678	1674	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.9169	554	1674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,042] [INFO] DFAST Taxonomy check result was written to GCF_013363755.1_ASM1336375v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:45,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:45,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:45,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/checkm_data
[2024-01-24 13:58:45,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:45,094] [INFO] Task started: CheckM
[2024-01-24 13:58:45,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013363755.1_ASM1336375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013363755.1_ASM1336375v1_genomic.fna/checkm_input GCF_013363755.1_ASM1336375v1_genomic.fna/checkm_result
[2024-01-24 14:00:09,575] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:09,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:09,593] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:09,594] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:09,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013363755.1_ASM1336375v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:09,594] [INFO] Task started: Blastn
[2024-01-24 14:00:09,594] [INFO] Running command: blastn -query GCF_013363755.1_ASM1336375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg305cbf1e-b965-4533-b408-eca23b876ef7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013363755.1_ASM1336375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:11,899] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:11,902] [INFO] Selected 11 target genomes.
[2024-01-24 14:00:11,903] [INFO] Target genome list was writen to GCF_013363755.1_ASM1336375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:11,926] [INFO] Task started: fastANI
[2024-01-24 14:00:11,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68b1473-d6de-418a-bff2-60ab86e3a9df/GCF_013363755.1_ASM1336375v1_genomic.fna.gz --refList GCF_013363755.1_ASM1336375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013363755.1_ASM1336375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:26,274] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:26,287] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:26,288] [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_013363755.1	s__Comamonas antarcticus	100.0	1673	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014204315.1	s__Comamonas konjaci_A	91.1393	1381	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706035.1	s__Comamonas sp902706035	87.54	1141	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413525.1	s__Comamonas sp018413525	87.2816	1183	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544075.1	s__Comamonas terrae	82.0613	834	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.748	730	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_003604195.1	s__Giesbergeria lacusdiani	81.3627	668	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	81.1518	747	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_014207955.1	s__Acidovorax soli_A	81.0883	882	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	80.996	871	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_014302995.1	s__Variovorax sp014302995	79.5058	715	1674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:26,290] [INFO] GTDB search result was written to GCF_013363755.1_ASM1336375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:26,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:26,295] [INFO] DFAST_QC result json was written to GCF_013363755.1_ASM1336375v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:26,295] [INFO] DFAST_QC completed!
[2024-01-24 14:00:26,295] [INFO] Total running time: 0h2m31s