[2024-01-25 19:31:51,350] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference
[2024-01-25 19:31:52,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,467] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg51b3baa7-c3e9-40ab-aa3a-e9fe276604e5/GCF_000373385.1_ASM37338v1_genomic.fna.gz | prodigal -d GCF_000373385.1_ASM37338v1_genomic.fna/cds.fna -a GCF_000373385.1_ASM37338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:01,584] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:01,584] [INFO] Task started: HMMsearch
[2024-01-25 19:32:01,584] [INFO] Running command: hmmsearch --tblout GCF_000373385.1_ASM37338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/reference_markers.hmm GCF_000373385.1_ASM37338v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:01,774] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:01,775] [INFO] Found 6/6 markers.
[2024-01-25 19:32:01,802] [INFO] Query marker FASTA was written to GCF_000373385.1_ASM37338v1_genomic.fna/markers.fasta
[2024-01-25 19:32:01,802] [INFO] Task started: Blastn
[2024-01-25 19:32:01,802] [INFO] Running command: blastn -query GCF_000373385.1_ASM37338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/reference_markers.fasta -out GCF_000373385.1_ASM37338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:02,665] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:02,668] [INFO] Selected 20 target genomes.
[2024-01-25 19:32:02,668] [INFO] Target genome list was writen to GCF_000373385.1_ASM37338v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:02,674] [INFO] Task started: fastANI
[2024-01-25 19:32:02,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b3baa7-c3e9-40ab-aa3a-e9fe276604e5/GCF_000373385.1_ASM37338v1_genomic.fna.gz --refList GCF_000373385.1_ASM37338v1_genomic.fna/target_genomes.txt --output GCF_000373385.1_ASM37338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:16,968] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:16,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:16,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:16,980] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:16,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:16,981] [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 thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	100.0	1056	1056	95	conclusive
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	83.9493	697	1056	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	78.7489	282	1056	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	78.6154	290	1056	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.9843	193	1056	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.9644	221	1056	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.9323	246	1056	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.8879	212	1056	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.7172	188	1056	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.6737	181	1056	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.5658	208	1056	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.5565	203	1056	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	77.501	202	1056	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	77.43	208	1056	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	77.3118	180	1056	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	77.2555	227	1056	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	77.1007	218	1056	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	77.0933	234	1056	95	below_threshold
Cupriavidus pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	76.785	151	1056	95	below_threshold
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	76.7593	154	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:16,982] [INFO] DFAST Taxonomy check result was written to GCF_000373385.1_ASM37338v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:16,983] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:16,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:16,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/checkm_data
[2024-01-25 19:32:16,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:17,017] [INFO] Task started: CheckM
[2024-01-25 19:32:17,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373385.1_ASM37338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373385.1_ASM37338v1_genomic.fna/checkm_input GCF_000373385.1_ASM37338v1_genomic.fna/checkm_result
[2024-01-25 19:32:47,221] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:47,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:47,244] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:47,244] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:47,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373385.1_ASM37338v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:47,245] [INFO] Task started: Blastn
[2024-01-25 19:32:47,245] [INFO] Running command: blastn -query GCF_000373385.1_ASM37338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803d0b2c-9dbc-48ad-b6c7-5b23b7c72e14/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373385.1_ASM37338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:48,849] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:48,852] [INFO] Selected 9 target genomes.
[2024-01-25 19:32:48,852] [INFO] Target genome list was writen to GCF_000373385.1_ASM37338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:48,859] [INFO] Task started: fastANI
[2024-01-25 19:32:48,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b3baa7-c3e9-40ab-aa3a-e9fe276604e5/GCF_000373385.1_ASM37338v1_genomic.fna.gz --refList GCF_000373385.1_ASM37338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373385.1_ASM37338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:55,437] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:55,444] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:55,444] [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_000373385.1	s__Thiobacillus thioparus	100.0	1056	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002343685.1	s__Thiobacillus denitrificans_A	92.4474	825	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.48	97.29	0.88	0.86	5	-
GCA_001899305.1	s__Thiobacillus sp001899305	92.3568	914	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	97.65	95.89	0.93	0.87	5	-
GCA_016195805.1	s__Thiobacillus sp016195805	87.2141	767	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899765.1	s__Thiobacillus sp001899765	86.1875	731	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.02	98.01	0.93	0.89	5	-
GCA_018820765.1	s__Thiobacillus sp018820765	84.6751	688	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_018262815.1	s__Thiobacillus sp018262815	84.1703	547	1056	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	83.9492	697	1056	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	83.9067	510	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:55,445] [INFO] GTDB search result was written to GCF_000373385.1_ASM37338v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:55,446] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:55,448] [INFO] DFAST_QC result json was written to GCF_000373385.1_ASM37338v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:55,449] [INFO] DFAST_QC completed!
[2024-01-25 19:32:55,449] [INFO] Total running time: 0h1m4s