[2023-06-28 15:14:11,707] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:14:11,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:14:11,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference
[2023-06-28 15:14:12,939] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:14:12,940] [INFO] Task started: Prodigal
[2023-06-28 15:14:12,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e92cbc-eb57-4d02-9776-64ca5488cc5c/GCA_027310195.1_ASM2731019v1_genomic.fna.gz | prodigal -d GCA_027310195.1_ASM2731019v1_genomic.fna/cds.fna -a GCA_027310195.1_ASM2731019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:14:19,277] [INFO] Task succeeded: Prodigal
[2023-06-28 15:14:19,277] [INFO] Task started: HMMsearch
[2023-06-28 15:14:19,277] [INFO] Running command: hmmsearch --tblout GCA_027310195.1_ASM2731019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/reference_markers.hmm GCA_027310195.1_ASM2731019v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:14:19,445] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:14:19,447] [INFO] Found 6/6 markers.
[2023-06-28 15:14:19,467] [INFO] Query marker FASTA was written to GCA_027310195.1_ASM2731019v1_genomic.fna/markers.fasta
[2023-06-28 15:14:19,467] [INFO] Task started: Blastn
[2023-06-28 15:14:19,467] [INFO] Running command: blastn -query GCA_027310195.1_ASM2731019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/reference_markers.fasta -out GCA_027310195.1_ASM2731019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:14:20,045] [INFO] Task succeeded: Blastn
[2023-06-28 15:14:20,048] [INFO] Selected 13 target genomes.
[2023-06-28 15:14:20,049] [INFO] Target genome list was writen to GCA_027310195.1_ASM2731019v1_genomic.fna/target_genomes.txt
[2023-06-28 15:14:20,051] [INFO] Task started: fastANI
[2023-06-28 15:14:20,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e92cbc-eb57-4d02-9776-64ca5488cc5c/GCA_027310195.1_ASM2731019v1_genomic.fna.gz --refList GCA_027310195.1_ASM2731019v1_genomic.fna/target_genomes.txt --output GCA_027310195.1_ASM2731019v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:14:27,534] [INFO] Task succeeded: fastANI
[2023-06-28 15:14:27,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:14:27,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:14:27,546] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2023-06-28 15:14:27,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 15:14:27,546] [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=DSM 8584	GCA_018853615.1	33059	33059	type	True	99.3122	675	756	95	conclusive
Acidithiobacillus caldus	strain=ATCC 51756	GCA_000175575.2	33059	33059	type	True	99.2917	693	756	95	conclusive
Acidithiobacillus caldus	strain=KU	GCA_018853545.1	33059	33059	type	True	99.2642	621	756	95	conclusive
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	77.3454	173	756	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	77.2268	137	756	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	76.8753	130	756	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	76.5467	85	756	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	76.5082	132	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:14:27,548] [INFO] DFAST Taxonomy check result was written to GCA_027310195.1_ASM2731019v1_genomic.fna/tc_result.tsv
[2023-06-28 15:14:27,548] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:14:27,549] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:14:27,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/checkm_data
[2023-06-28 15:14:27,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:14:27,578] [INFO] Task started: CheckM
[2023-06-28 15:14:27,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310195.1_ASM2731019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310195.1_ASM2731019v1_genomic.fna/checkm_input GCA_027310195.1_ASM2731019v1_genomic.fna/checkm_result
[2023-06-28 15:14:50,574] [INFO] Task succeeded: CheckM
[2023-06-28 15:14:50,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:14:50,593] [INFO] ===== Completeness check finished =====
[2023-06-28 15:14:50,593] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:14:50,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310195.1_ASM2731019v1_genomic.fna/markers.fasta)
[2023-06-28 15:14:50,594] [INFO] Task started: Blastn
[2023-06-28 15:14:50,594] [INFO] Running command: blastn -query GCA_027310195.1_ASM2731019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg106b8591-9563-41e4-b480-e8d0ce8b07fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310195.1_ASM2731019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:14:51,460] [INFO] Task succeeded: Blastn
[2023-06-28 15:14:51,462] [INFO] Selected 21 target genomes.
[2023-06-28 15:14:51,463] [INFO] Target genome list was writen to GCA_027310195.1_ASM2731019v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:14:51,485] [INFO] Task started: fastANI
[2023-06-28 15:14:51,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e92cbc-eb57-4d02-9776-64ca5488cc5c/GCA_027310195.1_ASM2731019v1_genomic.fna.gz --refList GCA_027310195.1_ASM2731019v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310195.1_ASM2731019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:15:03,561] [INFO] Task succeeded: fastANI
[2023-06-28 15:15:03,569] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:15:03,569] [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_000175575.2	s__Acidithiobacillus_A caldus	99.2917	693	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_A	95.0	99.11	98.61	0.89	0.82	17	conclusive
GCA_002341825.1	s__UBA2486 sp002341825	77.3551	111	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721225.1	s__Acidithiobacillus_B sulfuriphilus	77.3425	174	756	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_000021485.1	s__Acidithiobacillus ferrooxidans	77.2268	137	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	77.1822	125	756	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	77.0535	95	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_018854025.1	s__UBA2486 sp018854025	76.8975	148	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	99.54	99.39	0.91	0.89	6	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	76.8928	129	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_002847505.1	s__Acidithiobacillus sp002847505	76.5522	105	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	76.545	84	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
--------------------------------------------------------------------------------
[2023-06-28 15:15:03,570] [INFO] GTDB search result was written to GCA_027310195.1_ASM2731019v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:15:03,571] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:15:03,573] [INFO] DFAST_QC result json was written to GCA_027310195.1_ASM2731019v1_genomic.fna/dqc_result.json
[2023-06-28 15:15:03,573] [INFO] DFAST_QC completed!
[2023-06-28 15:15:03,573] [INFO] Total running time: 0h0m52s