[2023-06-29 13:30:08,695] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:30:08,698] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:30:08,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference
[2023-06-29 13:30:09,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:30:09,918] [INFO] Task started: Prodigal
[2023-06-29 13:30:09,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5686faf-1693-454e-b762-e583a2f6ae4e/GCA_021741495.1_ASM2174149v1_genomic.fna.gz | prodigal -d GCA_021741495.1_ASM2174149v1_genomic.fna/cds.fna -a GCA_021741495.1_ASM2174149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:30:19,187] [INFO] Task succeeded: Prodigal
[2023-06-29 13:30:19,188] [INFO] Task started: HMMsearch
[2023-06-29 13:30:19,188] [INFO] Running command: hmmsearch --tblout GCA_021741495.1_ASM2174149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/reference_markers.hmm GCA_021741495.1_ASM2174149v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:30:19,477] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:30:19,479] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf5686faf-1693-454e-b762-e583a2f6ae4e/GCA_021741495.1_ASM2174149v1_genomic.fna.gz]
[2023-06-29 13:30:19,511] [INFO] Query marker FASTA was written to GCA_021741495.1_ASM2174149v1_genomic.fna/markers.fasta
[2023-06-29 13:30:19,511] [INFO] Task started: Blastn
[2023-06-29 13:30:19,511] [INFO] Running command: blastn -query GCA_021741495.1_ASM2174149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/reference_markers.fasta -out GCA_021741495.1_ASM2174149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:30:20,113] [INFO] Task succeeded: Blastn
[2023-06-29 13:30:20,116] [INFO] Selected 8 target genomes.
[2023-06-29 13:30:20,117] [INFO] Target genome list was writen to GCA_021741495.1_ASM2174149v1_genomic.fna/target_genomes.txt
[2023-06-29 13:30:20,119] [INFO] Task started: fastANI
[2023-06-29 13:30:20,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5686faf-1693-454e-b762-e583a2f6ae4e/GCA_021741495.1_ASM2174149v1_genomic.fna.gz --refList GCA_021741495.1_ASM2174149v1_genomic.fna/target_genomes.txt --output GCA_021741495.1_ASM2174149v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:30:29,539] [INFO] Task succeeded: fastANI
[2023-06-29 13:30:29,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:30:29,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:30:29,549] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:30:29,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:30:29,549] [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
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	81.669	644	1017	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	81.548	667	1017	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	81.283	604	1017	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	77.9223	408	1017	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.4626	181	1017	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3322	213	1017	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3304	215	1017	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.9671	80	1017	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:30:29,552] [INFO] DFAST Taxonomy check result was written to GCA_021741495.1_ASM2174149v1_genomic.fna/tc_result.tsv
[2023-06-29 13:30:29,553] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:30:29,553] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:30:29,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/checkm_data
[2023-06-29 13:30:29,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:30:29,589] [INFO] Task started: CheckM
[2023-06-29 13:30:29,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021741495.1_ASM2174149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021741495.1_ASM2174149v1_genomic.fna/checkm_input GCA_021741495.1_ASM2174149v1_genomic.fna/checkm_result
[2023-06-29 13:31:02,436] [INFO] Task succeeded: CheckM
[2023-06-29 13:31:02,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 12.50%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-29 13:31:02,464] [INFO] ===== Completeness check finished =====
[2023-06-29 13:31:02,465] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:31:02,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021741495.1_ASM2174149v1_genomic.fna/markers.fasta)
[2023-06-29 13:31:02,465] [INFO] Task started: Blastn
[2023-06-29 13:31:02,466] [INFO] Running command: blastn -query GCA_021741495.1_ASM2174149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg134e05a4-0b1d-48d6-9d39-9ea6cdece37c/dqc_reference/reference_markers_gtdb.fasta -out GCA_021741495.1_ASM2174149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:31:03,129] [INFO] Task succeeded: Blastn
[2023-06-29 13:31:03,132] [INFO] Selected 13 target genomes.
[2023-06-29 13:31:03,132] [INFO] Target genome list was writen to GCA_021741495.1_ASM2174149v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:31:03,193] [INFO] Task started: fastANI
[2023-06-29 13:31:03,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5686faf-1693-454e-b762-e583a2f6ae4e/GCA_021741495.1_ASM2174149v1_genomic.fna.gz --refList GCA_021741495.1_ASM2174149v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021741495.1_ASM2174149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:31:15,691] [INFO] Task succeeded: fastANI
[2023-06-29 13:31:15,709] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:31:15,710] [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_004296935.1	s__Reyranella sp004296935	84.7493	723	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767945.1	s__Reyranella sp001767945	84.2442	589	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	83.3886	568	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	82.3876	489	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	81.8155	558	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772935.1	s__Reyranella sp009772935	81.7053	622	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	81.663	622	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_019039055.1	s__Reyranella sp019039055	81.6332	647	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297265.1	s__Reyranella sp004297265	81.6297	642	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240695.1	s__Reyranella sp018240695	81.2405	504	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_903832005.1	s__Reyranella aerosaccus_B	80.6645	579	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCA_903839865.1	s__Reyranella aerosaccus_A	80.6234	499	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.29	98.98	0.87	0.83	3	-
GCA_903915535.1	s__Reyranella aerosaccus_C	80.5464	551	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.05	99.05	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-29 13:31:15,712] [INFO] GTDB search result was written to GCA_021741495.1_ASM2174149v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:31:15,713] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:31:15,717] [INFO] DFAST_QC result json was written to GCA_021741495.1_ASM2174149v1_genomic.fna/dqc_result.json
[2023-06-29 13:31:15,717] [INFO] DFAST_QC completed!
[2023-06-29 13:31:15,718] [INFO] Total running time: 0h1m7s