[2023-06-29 23:16:23,934] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:16:23,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:16:23,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference
[2023-06-29 23:16:25,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:16:25,177] [INFO] Task started: Prodigal
[2023-06-29 23:16:25,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg39b02c3d-e7a5-4747-89d8-a8fc67639854/GCA_024709685.1_ASM2470968v1_genomic.fna.gz | prodigal -d GCA_024709685.1_ASM2470968v1_genomic.fna/cds.fna -a GCA_024709685.1_ASM2470968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:32,208] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:32,208] [INFO] Task started: HMMsearch
[2023-06-29 23:16:32,208] [INFO] Running command: hmmsearch --tblout GCA_024709685.1_ASM2470968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/reference_markers.hmm GCA_024709685.1_ASM2470968v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:32,416] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:32,417] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg39b02c3d-e7a5-4747-89d8-a8fc67639854/GCA_024709685.1_ASM2470968v1_genomic.fna.gz]
[2023-06-29 23:16:32,444] [INFO] Query marker FASTA was written to GCA_024709685.1_ASM2470968v1_genomic.fna/markers.fasta
[2023-06-29 23:16:32,445] [INFO] Task started: Blastn
[2023-06-29 23:16:32,445] [INFO] Running command: blastn -query GCA_024709685.1_ASM2470968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/reference_markers.fasta -out GCA_024709685.1_ASM2470968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:33,160] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:33,165] [INFO] Selected 13 target genomes.
[2023-06-29 23:16:33,165] [INFO] Target genome list was writen to GCA_024709685.1_ASM2470968v1_genomic.fna/target_genomes.txt
[2023-06-29 23:16:33,167] [INFO] Task started: fastANI
[2023-06-29 23:16:33,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b02c3d-e7a5-4747-89d8-a8fc67639854/GCA_024709685.1_ASM2470968v1_genomic.fna.gz --refList GCA_024709685.1_ASM2470968v1_genomic.fna/target_genomes.txt --output GCA_024709685.1_ASM2470968v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:16:42,641] [INFO] Task succeeded: fastANI
[2023-06-29 23:16:42,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:16:42,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:16:42,652] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:16:42,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:16:42,652] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	84.1126	487	758	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	83.0582	452	758	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.9042	160	758	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	77.3393	160	758	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.3205	151	758	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.3012	152	758	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	77.2685	169	758	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	77.0752	176	758	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.9742	99	758	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.8299	169	758	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	76.2842	72	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:16:42,655] [INFO] DFAST Taxonomy check result was written to GCA_024709685.1_ASM2470968v1_genomic.fna/tc_result.tsv
[2023-06-29 23:16:42,655] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:16:42,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:16:42,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/checkm_data
[2023-06-29 23:16:42,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:16:42,690] [INFO] Task started: CheckM
[2023-06-29 23:16:42,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024709685.1_ASM2470968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024709685.1_ASM2470968v1_genomic.fna/checkm_input GCA_024709685.1_ASM2470968v1_genomic.fna/checkm_result
[2023-06-29 23:17:09,640] [INFO] Task succeeded: CheckM
[2023-06-29 23:17:09,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:17:09,666] [INFO] ===== Completeness check finished =====
[2023-06-29 23:17:09,666] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:17:09,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024709685.1_ASM2470968v1_genomic.fna/markers.fasta)
[2023-06-29 23:17:09,667] [INFO] Task started: Blastn
[2023-06-29 23:17:09,668] [INFO] Running command: blastn -query GCA_024709685.1_ASM2470968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f95242d-ad20-4329-8258-ffbc7e973e7d/dqc_reference/reference_markers_gtdb.fasta -out GCA_024709685.1_ASM2470968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:10,799] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:10,804] [INFO] Selected 13 target genomes.
[2023-06-29 23:17:10,804] [INFO] Target genome list was writen to GCA_024709685.1_ASM2470968v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:17:10,807] [INFO] Task started: fastANI
[2023-06-29 23:17:10,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b02c3d-e7a5-4747-89d8-a8fc67639854/GCA_024709685.1_ASM2470968v1_genomic.fna.gz --refList GCA_024709685.1_ASM2470968v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024709685.1_ASM2470968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:17:18,685] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:18,703] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:17:18,704] [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_001897675.1	s__Thiobacillus sp001897675	84.559	462	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.41	95.18	0.77	0.76	3	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	84.531	509	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_018820765.1	s__Thiobacillus sp018820765	84.4171	475	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_016195805.1	s__Thiobacillus sp016195805	84.2282	435	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376425.1	s__Thiobacillus denitrificans	84.1126	487	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256995.1	s__Thiobacillus sp002256995	83.6511	503	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.94	97.93	0.93	0.88	3	-
GCA_011391285.1	s__Thiobacillus sp011391285	83.5731	409	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262815.1	s__Thiobacillus sp018262815	83.5507	380	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003510325.1	s__Thiobacillus sp003510325	83.3326	359	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
GCF_000373385.1	s__Thiobacillus thioparus	83.0716	451	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899305.1	s__Thiobacillus sp001899305	82.9394	457	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCA_002343685.1	s__Thiobacillus denitrificans_A	82.6763	434	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCA_001899765.1	s__Thiobacillus sp001899765	82.5305	442	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.02	98.01	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2023-06-29 23:17:18,706] [INFO] GTDB search result was written to GCA_024709685.1_ASM2470968v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:17:18,706] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:17:18,711] [INFO] DFAST_QC result json was written to GCA_024709685.1_ASM2470968v1_genomic.fna/dqc_result.json
[2023-06-29 23:17:18,711] [INFO] DFAST_QC completed!
[2023-06-29 23:17:18,712] [INFO] Total running time: 0h0m55s