[2024-01-24 11:12:36,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference
[2024-01-24 11:12:38,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,666] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg21439679-2208-42b1-ac51-ade4d41cc7d7/GCF_022809125.1_ASM2280912v1_genomic.fna.gz | prodigal -d GCF_022809125.1_ASM2280912v1_genomic.fna/cds.fna -a GCF_022809125.1_ASM2280912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:54,593] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:54,594] [INFO] Task started: HMMsearch
[2024-01-24 11:12:54,594] [INFO] Running command: hmmsearch --tblout GCF_022809125.1_ASM2280912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/reference_markers.hmm GCF_022809125.1_ASM2280912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:54,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:54,822] [INFO] Found 6/6 markers.
[2024-01-24 11:12:54,860] [INFO] Query marker FASTA was written to GCF_022809125.1_ASM2280912v1_genomic.fna/markers.fasta
[2024-01-24 11:12:54,861] [INFO] Task started: Blastn
[2024-01-24 11:12:54,861] [INFO] Running command: blastn -query GCF_022809125.1_ASM2280912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/reference_markers.fasta -out GCF_022809125.1_ASM2280912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:55,909] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:55,912] [INFO] Selected 23 target genomes.
[2024-01-24 11:12:55,912] [INFO] Target genome list was writen to GCF_022809125.1_ASM2280912v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:55,944] [INFO] Task started: fastANI
[2024-01-24 11:12:55,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg21439679-2208-42b1-ac51-ade4d41cc7d7/GCF_022809125.1_ASM2280912v1_genomic.fna.gz --refList GCF_022809125.1_ASM2280912v1_genomic.fna/target_genomes.txt --output GCF_022809125.1_ASM2280912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,293] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:20,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:20,311] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:20,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:20,312] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	83.3532	808	1643	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.6104	731	1643	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	82.4569	876	1643	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	82.4177	895	1643	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	82.3766	867	1643	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.3218	840	1643	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	82.3055	760	1643	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	82.3024	878	1643	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.2916	795	1643	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	82.0992	886	1643	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	81.8532	753	1643	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	81.7329	772	1643	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.6749	740	1643	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	81.6159	902	1643	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.5842	739	1643	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.4413	763	1643	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	81.3054	704	1643	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	81.2599	784	1643	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.1475	761	1643	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.0818	670	1643	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.0617	710	1643	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	80.1055	672	1643	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.9561	549	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,313] [INFO] DFAST Taxonomy check result was written to GCF_022809125.1_ASM2280912v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:20,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:20,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:20,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/checkm_data
[2024-01-24 11:13:20,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:20,368] [INFO] Task started: CheckM
[2024-01-24 11:13:20,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022809125.1_ASM2280912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022809125.1_ASM2280912v1_genomic.fna/checkm_input GCF_022809125.1_ASM2280912v1_genomic.fna/checkm_result
[2024-01-24 11:14:20,629] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:20,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:20,648] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:20,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:20,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022809125.1_ASM2280912v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:20,649] [INFO] Task started: Blastn
[2024-01-24 11:14:20,649] [INFO] Running command: blastn -query GCF_022809125.1_ASM2280912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32988612-858f-4d3c-bb12-6fec8ce29c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_022809125.1_ASM2280912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:22,924] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:22,927] [INFO] Selected 28 target genomes.
[2024-01-24 11:14:22,928] [INFO] Target genome list was writen to GCF_022809125.1_ASM2280912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:22,961] [INFO] Task started: fastANI
[2024-01-24 11:14:22,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg21439679-2208-42b1-ac51-ade4d41cc7d7/GCF_022809125.1_ASM2280912v1_genomic.fna.gz --refList GCF_022809125.1_ASM2280912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022809125.1_ASM2280912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:53,130] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:53,150] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:53,151] [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
GCA_005503335.1	s__SCMQ01 sp005503335	83.6364	776	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000215705.1	s__Ramlibacter tataouinensis	83.3371	810	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191525.1	s__Ramlibacter sp016191525	83.1273	873	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	82.7839	807	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	82.6276	822	1643	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_001591365.1	s__Variovorax paradoxus	82.4055	896	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.93	98.38	0.94	0.90	4	-
GCF_013087525.1	s__Ramlibacter sp013087525	82.405	835	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	82.4018	851	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	82.3808	662	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013778345.1	s__Ramlibacter sp013778345	82.3752	868	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004217005.1	s__Variovorax sp004217005	82.325	847	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.70	99.70	0.95	0.95	2	-
GCF_003951285.1	s__Variovorax beijingensis	82.3023	881	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.27	99.27	0.92	0.92	2	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	82.2781	795	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	82.2603	762	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCF_014207955.1	s__Acidovorax soli_A	82.1524	902	1643	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	82.0254	894	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCA_019218755.1	s__Acidovorax sp019218755	81.9928	832	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_001432305.1	s__Hylemonella sp001432305	81.9909	677	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428665.1	s__Acidovorax sp001428665	81.931	875	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCA_004144865.1	s__Ramlibacter sp004144865	81.9254	725	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	81.8858	737	1643	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_013408765.1	s__Acidovorax sp013408765	81.8685	872	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842205.1	s__PHCI01 sp002842205	81.8034	726	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	81.7328	692	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765735.1	s__Variovorax sp009765735	81.6131	793	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	81.3811	709	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_001770955.1	s__Giesbergeria sp001770955	81.3535	599	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_003350475.1	s__Pseudacidovorax intermedius	81.292	839	1643	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:53,187] [INFO] GTDB search result was written to GCF_022809125.1_ASM2280912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:53,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:53,192] [INFO] DFAST_QC result json was written to GCF_022809125.1_ASM2280912v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:53,192] [INFO] DFAST_QC completed!
[2024-01-24 11:14:53,192] [INFO] Total running time: 0h2m17s