[2023-06-29 02:27:46,279] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:27:46,281] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:27:46,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference
[2023-06-29 02:27:47,490] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:27:47,491] [INFO] Task started: Prodigal
[2023-06-29 02:27:47,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e339691-1b25-426c-b355-d401950f7ed3/GCA_020722245.1_ASM2072224v1_genomic.fna.gz | prodigal -d GCA_020722245.1_ASM2072224v1_genomic.fna/cds.fna -a GCA_020722245.1_ASM2072224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:27:52,661] [INFO] Task succeeded: Prodigal
[2023-06-29 02:27:52,661] [INFO] Task started: HMMsearch
[2023-06-29 02:27:52,661] [INFO] Running command: hmmsearch --tblout GCA_020722245.1_ASM2072224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/reference_markers.hmm GCA_020722245.1_ASM2072224v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:27:52,903] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:27:52,905] [INFO] Found 6/6 markers.
[2023-06-29 02:27:52,930] [INFO] Query marker FASTA was written to GCA_020722245.1_ASM2072224v1_genomic.fna/markers.fasta
[2023-06-29 02:27:52,930] [INFO] Task started: Blastn
[2023-06-29 02:27:52,930] [INFO] Running command: blastn -query GCA_020722245.1_ASM2072224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/reference_markers.fasta -out GCA_020722245.1_ASM2072224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:27:53,519] [INFO] Task succeeded: Blastn
[2023-06-29 02:27:53,525] [INFO] Selected 27 target genomes.
[2023-06-29 02:27:53,525] [INFO] Target genome list was writen to GCA_020722245.1_ASM2072224v1_genomic.fna/target_genomes.txt
[2023-06-29 02:27:53,529] [INFO] Task started: fastANI
[2023-06-29 02:27:53,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e339691-1b25-426c-b355-d401950f7ed3/GCA_020722245.1_ASM2072224v1_genomic.fna.gz --refList GCA_020722245.1_ASM2072224v1_genomic.fna/target_genomes.txt --output GCA_020722245.1_ASM2072224v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:28:11,132] [INFO] Task succeeded: fastANI
[2023-06-29 02:28:11,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:28:11,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:28:11,140] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:28:11,140] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:28:11,140] [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
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.564	72	643	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.0956	60	643	95	below_threshold
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	76.0635	53	643	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:28:11,142] [INFO] DFAST Taxonomy check result was written to GCA_020722245.1_ASM2072224v1_genomic.fna/tc_result.tsv
[2023-06-29 02:28:11,143] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:28:11,143] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:28:11,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/checkm_data
[2023-06-29 02:28:11,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:28:11,173] [INFO] Task started: CheckM
[2023-06-29 02:28:11,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020722245.1_ASM2072224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020722245.1_ASM2072224v1_genomic.fna/checkm_input GCA_020722245.1_ASM2072224v1_genomic.fna/checkm_result
[2023-06-29 02:28:33,447] [INFO] Task succeeded: CheckM
[2023-06-29 02:28:33,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:28:33,471] [INFO] ===== Completeness check finished =====
[2023-06-29 02:28:33,471] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:28:33,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020722245.1_ASM2072224v1_genomic.fna/markers.fasta)
[2023-06-29 02:28:33,472] [INFO] Task started: Blastn
[2023-06-29 02:28:33,472] [INFO] Running command: blastn -query GCA_020722245.1_ASM2072224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb38677c8-c15d-407a-ad16-7e140edc1727/dqc_reference/reference_markers_gtdb.fasta -out GCA_020722245.1_ASM2072224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:28:34,254] [INFO] Task succeeded: Blastn
[2023-06-29 02:28:34,259] [INFO] Selected 32 target genomes.
[2023-06-29 02:28:34,259] [INFO] Target genome list was writen to GCA_020722245.1_ASM2072224v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:28:34,278] [INFO] Task started: fastANI
[2023-06-29 02:28:34,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e339691-1b25-426c-b355-d401950f7ed3/GCA_020722245.1_ASM2072224v1_genomic.fna.gz --refList GCA_020722245.1_ASM2072224v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020722245.1_ASM2072224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:28:52,595] [INFO] Task succeeded: fastANI
[2023-06-29 02:28:52,605] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:28:52,606] [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_003597945.1	s__SURF-33 sp003597945	77.0795	102	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390415.1	s__SURF-3 sp011390415	76.5946	92	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018405.1	s__Desulfosudis oleovorans	76.564	72	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237465.1	s__SURF-3 sp014237465	76.3539	80	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011042305.1	s__UBA2174 sp011042305	76.308	65	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599885.1	s__SURF-3 sp003599885	76.299	78	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018224315.1	s__Desulfosalsimonas sp018224315	76.2975	61	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390465.1	s__SURF-3 sp011390465	76.2493	113	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__SURF-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335195.1	s__Desulfosalsimonas sp018335195	76.0108	62	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas	95.0	99.35	99.35	0.95	0.95	2	-
GCA_016342285.1	s__JAEINQ01 sp016342285	75.7617	65	643	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:28:52,608] [INFO] GTDB search result was written to GCA_020722245.1_ASM2072224v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:28:52,609] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:28:52,613] [INFO] DFAST_QC result json was written to GCA_020722245.1_ASM2072224v1_genomic.fna/dqc_result.json
[2023-06-29 02:28:52,613] [INFO] DFAST_QC completed!
[2023-06-29 02:28:52,614] [INFO] Total running time: 0h1m6s