[2023-06-28 00:18:39,740] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:18:39,742] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:18:39,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference
[2023-06-28 00:18:41,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:18:41,086] [INFO] Task started: Prodigal
[2023-06-28 00:18:41,086] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3f84d81-3957-4d74-84f1-7e3160f882ca/GCA_027494545.1_ASM2749454v1_genomic.fna.gz | prodigal -d GCA_027494545.1_ASM2749454v1_genomic.fna/cds.fna -a GCA_027494545.1_ASM2749454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:18:54,332] [INFO] Task succeeded: Prodigal
[2023-06-28 00:18:54,333] [INFO] Task started: HMMsearch
[2023-06-28 00:18:54,333] [INFO] Running command: hmmsearch --tblout GCA_027494545.1_ASM2749454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/reference_markers.hmm GCA_027494545.1_ASM2749454v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:18:54,668] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:18:54,670] [INFO] Found 6/6 markers.
[2023-06-28 00:18:54,710] [INFO] Query marker FASTA was written to GCA_027494545.1_ASM2749454v1_genomic.fna/markers.fasta
[2023-06-28 00:18:54,711] [INFO] Task started: Blastn
[2023-06-28 00:18:54,711] [INFO] Running command: blastn -query GCA_027494545.1_ASM2749454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/reference_markers.fasta -out GCA_027494545.1_ASM2749454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:18:55,974] [INFO] Task succeeded: Blastn
[2023-06-28 00:18:55,979] [INFO] Selected 21 target genomes.
[2023-06-28 00:18:55,980] [INFO] Target genome list was writen to GCA_027494545.1_ASM2749454v1_genomic.fna/target_genomes.txt
[2023-06-28 00:18:55,988] [INFO] Task started: fastANI
[2023-06-28 00:18:55,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3f84d81-3957-4d74-84f1-7e3160f882ca/GCA_027494545.1_ASM2749454v1_genomic.fna.gz --refList GCA_027494545.1_ASM2749454v1_genomic.fna/target_genomes.txt --output GCA_027494545.1_ASM2749454v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:19:19,738] [INFO] Task succeeded: fastANI
[2023-06-28 00:19:19,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:19:19,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:19:19,760] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:19:19,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:19:19,760] [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
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	82.0439	820	1336	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.9893	835	1336	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.9691	694	1336	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.9191	766	1336	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.5193	697	1336	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	81.0689	619	1336	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.967	595	1336	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	80.8577	704	1336	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	80.5679	653	1336	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.5594	633	1336	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.5184	576	1336	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	80.5033	648	1336	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.3344	586	1336	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	80.2693	672	1336	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.0826	661	1336	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0606	586	1336	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.96	755	1336	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.8108	616	1336	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.7977	601	1336	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.524	569	1336	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.436	609	1336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:19:19,762] [INFO] DFAST Taxonomy check result was written to GCA_027494545.1_ASM2749454v1_genomic.fna/tc_result.tsv
[2023-06-28 00:19:19,764] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:19:19,764] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:19:19,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/checkm_data
[2023-06-28 00:19:19,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:19:19,808] [INFO] Task started: CheckM
[2023-06-28 00:19:19,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027494545.1_ASM2749454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027494545.1_ASM2749454v1_genomic.fna/checkm_input GCA_027494545.1_ASM2749454v1_genomic.fna/checkm_result
[2023-06-28 00:20:06,685] [INFO] Task succeeded: CheckM
[2023-06-28 00:20:06,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:20:06,712] [INFO] ===== Completeness check finished =====
[2023-06-28 00:20:06,712] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:20:06,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027494545.1_ASM2749454v1_genomic.fna/markers.fasta)
[2023-06-28 00:20:06,713] [INFO] Task started: Blastn
[2023-06-28 00:20:06,713] [INFO] Running command: blastn -query GCA_027494545.1_ASM2749454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee71a02d-e592-4bf9-bd1f-a8d2b612c3aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_027494545.1_ASM2749454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:20:08,956] [INFO] Task succeeded: Blastn
[2023-06-28 00:20:08,960] [INFO] Selected 11 target genomes.
[2023-06-28 00:20:08,960] [INFO] Target genome list was writen to GCA_027494545.1_ASM2749454v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:20:08,969] [INFO] Task started: fastANI
[2023-06-28 00:20:08,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3f84d81-3957-4d74-84f1-7e3160f882ca/GCA_027494545.1_ASM2749454v1_genomic.fna.gz --refList GCA_027494545.1_ASM2749454v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027494545.1_ASM2749454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:20:22,129] [INFO] Task succeeded: fastANI
[2023-06-28 00:20:22,146] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:20:22,147] [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	97.018	1232	1336	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	90.8886	1185	1336	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	87.5614	1045	1336	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	87.2711	1057	1336	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	81.9585	761	1336	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	81.6497	665	1336	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	81.3564	621	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	81.1626	789	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	81.1015	671	1336	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_003053545.1	s__Acidovorax sp003053545	81.0598	785	1336	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	79.6386	631	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:20:22,149] [INFO] GTDB search result was written to GCA_027494545.1_ASM2749454v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:20:22,149] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:20:22,154] [INFO] DFAST_QC result json was written to GCA_027494545.1_ASM2749454v1_genomic.fna/dqc_result.json
[2023-06-28 00:20:22,154] [INFO] DFAST_QC completed!
[2023-06-28 00:20:22,154] [INFO] Total running time: 0h1m42s