[2023-06-30 15:35:37,915] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:35:37,917] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:35:37,918] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference
[2023-06-30 15:35:41,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:35:41,124] [INFO] Task started: Prodigal
[2023-06-30 15:35:41,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg154fc21a-f616-4421-9056-4c495830453c/GCA_024708965.1_ASM2470896v1_genomic.fna.gz | prodigal -d GCA_024708965.1_ASM2470896v1_genomic.fna/cds.fna -a GCA_024708965.1_ASM2470896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:35:50,438] [INFO] Task succeeded: Prodigal
[2023-06-30 15:35:50,438] [INFO] Task started: HMMsearch
[2023-06-30 15:35:50,438] [INFO] Running command: hmmsearch --tblout GCA_024708965.1_ASM2470896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/reference_markers.hmm GCA_024708965.1_ASM2470896v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:35:50,724] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:35:50,726] [INFO] Found 6/6 markers.
[2023-06-30 15:35:50,762] [INFO] Query marker FASTA was written to GCA_024708965.1_ASM2470896v1_genomic.fna/markers.fasta
[2023-06-30 15:35:50,763] [INFO] Task started: Blastn
[2023-06-30 15:35:50,763] [INFO] Running command: blastn -query GCA_024708965.1_ASM2470896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/reference_markers.fasta -out GCA_024708965.1_ASM2470896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:35:51,761] [INFO] Task succeeded: Blastn
[2023-06-30 15:35:51,765] [INFO] Selected 28 target genomes.
[2023-06-30 15:35:51,765] [INFO] Target genome list was writen to GCA_024708965.1_ASM2470896v1_genomic.fna/target_genomes.txt
[2023-06-30 15:35:51,766] [INFO] Task started: fastANI
[2023-06-30 15:35:51,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg154fc21a-f616-4421-9056-4c495830453c/GCA_024708965.1_ASM2470896v1_genomic.fna.gz --refList GCA_024708965.1_ASM2470896v1_genomic.fna/target_genomes.txt --output GCA_024708965.1_ASM2470896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:36:13,465] [INFO] Task succeeded: fastANI
[2023-06-30 15:36:13,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:36:13,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:36:13,491] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:36:13,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:36:13,492] [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 soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.1809	408	711	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	81.8322	418	711	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	81.827	465	711	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	81.5287	436	711	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.4253	445	711	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.3077	413	711	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	81.2908	439	711	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.2229	375	711	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.0972	385	711	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	81.0659	426	711	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.9863	410	711	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.9819	411	711	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.6945	407	711	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	80.6292	407	711	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.6282	381	711	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.5754	384	711	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	80.415	389	711	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	80.4043	384	711	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	80.3559	393	711	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.2461	348	711	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.2453	368	711	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.051	324	711	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	79.9548	401	711	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.6517	302	711	95	below_threshold
Verminephrobacter aporrectodeae subsp. tuberculatae	strain=At4	GCA_000193225.2	1110392	1110389	type	True	79.6365	265	711	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.3386	311	711	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.0755	263	711	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.0074	284	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:36:13,494] [INFO] DFAST Taxonomy check result was written to GCA_024708965.1_ASM2470896v1_genomic.fna/tc_result.tsv
[2023-06-30 15:36:13,495] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:36:13,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:36:13,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/checkm_data
[2023-06-30 15:36:13,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:36:13,536] [INFO] Task started: CheckM
[2023-06-30 15:36:13,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708965.1_ASM2470896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708965.1_ASM2470896v1_genomic.fna/checkm_input GCA_024708965.1_ASM2470896v1_genomic.fna/checkm_result
[2023-06-30 15:36:48,103] [INFO] Task succeeded: CheckM
[2023-06-30 15:36:48,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 5.01%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 15:36:48,129] [INFO] ===== Completeness check finished =====
[2023-06-30 15:36:48,129] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:36:48,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708965.1_ASM2470896v1_genomic.fna/markers.fasta)
[2023-06-30 15:36:48,130] [INFO] Task started: Blastn
[2023-06-30 15:36:48,130] [INFO] Running command: blastn -query GCA_024708965.1_ASM2470896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafddc68-0896-408c-a85c-06d3bc0b4a3e/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708965.1_ASM2470896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:36:50,171] [INFO] Task succeeded: Blastn
[2023-06-30 15:36:50,194] [INFO] Selected 15 target genomes.
[2023-06-30 15:36:50,194] [INFO] Target genome list was writen to GCA_024708965.1_ASM2470896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:36:50,200] [INFO] Task started: fastANI
[2023-06-30 15:36:50,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg154fc21a-f616-4421-9056-4c495830453c/GCA_024708965.1_ASM2470896v1_genomic.fna.gz --refList GCA_024708965.1_ASM2470896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708965.1_ASM2470896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:37:01,927] [INFO] Task succeeded: fastANI
[2023-06-30 15:37:01,952] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:37:01,952] [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_010020825.1	s__Giesbergeria sp010020825	97.377	635	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	conclusive
GCA_016192425.1	s__Giesbergeria sp016192425	89.4968	571	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	85.2115	542	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	84.8567	531	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCA_001770955.1	s__Giesbergeria sp001770955	84.1636	507	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_900107605.1	s__Acidovorax soli	82.1896	410	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCF_014489595.1	s__Acidovorax_F monticola	81.9382	454	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCA_019218755.1	s__Acidovorax sp019218755	81.9238	464	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_014207955.1	s__Acidovorax soli_A	81.7636	484	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.5961	411	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_019219095.1	s__Acidovorax sp019219095	81.4266	446	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	81.3405	396	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCA_001724785.1	s__Giesbergeria sp001724785	80.9872	340	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269065.1	s__Acidovorax_A anthurii	80.7148	405	711	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_014637085.1	s__Comamonas phosphati	80.23	349	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:37:01,954] [INFO] GTDB search result was written to GCA_024708965.1_ASM2470896v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:37:01,955] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:37:01,960] [INFO] DFAST_QC result json was written to GCA_024708965.1_ASM2470896v1_genomic.fna/dqc_result.json
[2023-06-30 15:37:01,960] [INFO] DFAST_QC completed!
[2023-06-30 15:37:01,960] [INFO] Total running time: 0h1m24s