[2024-01-24 12:36:50,184] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:50,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:50,186] [INFO] DQC Reference Directory: /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference
[2024-01-24 12:36:52,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:52,572] [INFO] Task started: Prodigal
[2024-01-24 12:36:52,572] [INFO] Running command: gunzip -c /var/lib/cwl/stge369f3c0-3617-413f-8e37-360618a0d7c0/GCF_018854015.1_ASM1885401v1_genomic.fna.gz | prodigal -d GCF_018854015.1_ASM1885401v1_genomic.fna/cds.fna -a GCF_018854015.1_ASM1885401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:00,969] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:00,969] [INFO] Task started: HMMsearch
[2024-01-24 12:37:00,969] [INFO] Running command: hmmsearch --tblout GCF_018854015.1_ASM1885401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/reference_markers.hmm GCF_018854015.1_ASM1885401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:01,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:01,148] [INFO] Found 6/6 markers.
[2024-01-24 12:37:01,174] [INFO] Query marker FASTA was written to GCF_018854015.1_ASM1885401v1_genomic.fna/markers.fasta
[2024-01-24 12:37:01,174] [INFO] Task started: Blastn
[2024-01-24 12:37:01,174] [INFO] Running command: blastn -query GCF_018854015.1_ASM1885401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/reference_markers.fasta -out GCF_018854015.1_ASM1885401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:02,647] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:02,650] [INFO] Selected 26 target genomes.
[2024-01-24 12:37:02,651] [INFO] Target genome list was writen to GCF_018854015.1_ASM1885401v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:02,938] [INFO] Task started: fastANI
[2024-01-24 12:37:02,939] [INFO] Running command: fastANI --query /var/lib/cwl/stge369f3c0-3617-413f-8e37-360618a0d7c0/GCF_018854015.1_ASM1885401v1_genomic.fna.gz --refList GCF_018854015.1_ASM1885401v1_genomic.fna/target_genomes.txt --output GCF_018854015.1_ASM1885401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:15,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:15,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:15,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:15,329] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:15,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:15,329] [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
Acidithiobacillus caldus	strain=ATCC 51756	GCA_000175575.2	33059	33059	type	True	77.6338	158	865	95	below_threshold
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	77.4402	100	865	95	below_threshold
Acidithiobacillus caldus	strain=DSM 8584	GCA_018853615.1	33059	33059	type	True	77.3387	154	865	95	below_threshold
Acidithiobacillus caldus	strain=KU	GCA_018853545.1	33059	33059	type	True	77.315	152	865	95	below_threshold
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	77.2968	119	865	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	77.216	107	865	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	77.1096	115	865	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	77.0123	111	865	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	76.4761	73	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:15,331] [INFO] DFAST Taxonomy check result was written to GCF_018854015.1_ASM1885401v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:15,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:15,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:15,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/checkm_data
[2024-01-24 12:37:15,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:15,360] [INFO] Task started: CheckM
[2024-01-24 12:37:15,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018854015.1_ASM1885401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018854015.1_ASM1885401v1_genomic.fna/checkm_input GCF_018854015.1_ASM1885401v1_genomic.fna/checkm_result
[2024-01-24 12:37:42,966] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:42,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:42,991] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:42,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:42,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018854015.1_ASM1885401v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:42,992] [INFO] Task started: Blastn
[2024-01-24 12:37:42,992] [INFO] Running command: blastn -query GCF_018854015.1_ASM1885401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga35819c8-b0c5-4679-95af-64e5baa3b401/dqc_reference/reference_markers_gtdb.fasta -out GCF_018854015.1_ASM1885401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:43,938] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:43,943] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:43,943] [INFO] Target genome list was writen to GCF_018854015.1_ASM1885401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:44,053] [INFO] Task started: fastANI
[2024-01-24 12:37:44,054] [INFO] Running command: fastANI --query /var/lib/cwl/stge369f3c0-3617-413f-8e37-360618a0d7c0/GCF_018854015.1_ASM1885401v1_genomic.fna.gz --refList GCF_018854015.1_ASM1885401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018854015.1_ASM1885401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:53,961] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,970] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:53,970] [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_018854025.1	s__UBA2486 sp018854025	99.9822	853	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	99.54	99.39	0.91	0.89	6	conclusive
GCA_002341825.1	s__UBA2486 sp002341825	78.0128	189	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853465.1	s__Acidithiobacillus sp018853465	77.7391	111	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
GCF_000175575.2	s__Acidithiobacillus_A caldus	77.6461	161	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_A	95.0	99.11	98.61	0.89	0.82	17	-
GCF_003721225.1	s__Acidithiobacillus_B sulfuriphilus	77.2744	120	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	77.194	108	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	77.09	116	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	76.9929	112	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_015100155.1	s__Acidithiobacillus sp015100155	76.7587	87	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	76.7393	110	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	76.7392	104	865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,972] [INFO] GTDB search result was written to GCF_018854015.1_ASM1885401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:53,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:53,975] [INFO] DFAST_QC result json was written to GCF_018854015.1_ASM1885401v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:53,976] [INFO] DFAST_QC completed!
[2024-01-24 12:37:53,976] [INFO] Total running time: 0h1m4s