[2024-01-24 13:49:30,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,602] [INFO] DQC Reference Directory: /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference
[2024-01-24 13:49:31,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,919] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bda3206-40f5-42bb-816c-7d47973fc08e/GCF_000175575.2_ASM17557v2_genomic.fna.gz | prodigal -d GCF_000175575.2_ASM17557v2_genomic.fna/cds.fna -a GCF_000175575.2_ASM17557v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:41,997] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:41,997] [INFO] Task started: HMMsearch
[2024-01-24 13:49:41,997] [INFO] Running command: hmmsearch --tblout GCF_000175575.2_ASM17557v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/reference_markers.hmm GCF_000175575.2_ASM17557v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,303] [INFO] Found 6/6 markers.
[2024-01-24 13:49:42,334] [INFO] Query marker FASTA was written to GCF_000175575.2_ASM17557v2_genomic.fna/markers.fasta
[2024-01-24 13:49:42,334] [INFO] Task started: Blastn
[2024-01-24 13:49:42,334] [INFO] Running command: blastn -query GCF_000175575.2_ASM17557v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/reference_markers.fasta -out GCF_000175575.2_ASM17557v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,992] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,996] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:42,996] [INFO] Target genome list was writen to GCF_000175575.2_ASM17557v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,008] [INFO] Task started: fastANI
[2024-01-24 13:49:43,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bda3206-40f5-42bb-816c-7d47973fc08e/GCF_000175575.2_ASM17557v2_genomic.fna.gz --refList GCF_000175575.2_ASM17557v2_genomic.fna/target_genomes.txt --output GCF_000175575.2_ASM17557v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:57,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:57,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:57,939] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:57,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:57,940] [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	100.0	992	994	95	conclusive
Acidithiobacillus caldus	strain=DSM 8584	GCA_018853615.1	33059	33059	type	True	99.8387	875	994	95	conclusive
Acidithiobacillus caldus	strain=KU	GCA_018853545.1	33059	33059	type	True	99.768	811	994	95	conclusive
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	77.7761	134	994	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	77.6422	135	994	95	below_threshold
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	77.5979	180	994	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	77.5542	135	994	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	77.4843	109	994	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.97	57	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,948] [INFO] DFAST Taxonomy check result was written to GCF_000175575.2_ASM17557v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:57,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:57,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:57,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/checkm_data
[2024-01-24 13:49:57,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:57,982] [INFO] Task started: CheckM
[2024-01-24 13:49:57,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000175575.2_ASM17557v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000175575.2_ASM17557v2_genomic.fna/checkm_input GCF_000175575.2_ASM17557v2_genomic.fna/checkm_result
[2024-01-24 13:50:31,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,891] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,891] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000175575.2_ASM17557v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,892] [INFO] Task started: Blastn
[2024-01-24 13:50:31,892] [INFO] Running command: blastn -query GCF_000175575.2_ASM17557v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge48502e1-d1ad-498e-a981-f253ee85ff79/dqc_reference/reference_markers_gtdb.fasta -out GCF_000175575.2_ASM17557v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:32,792] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:32,795] [INFO] Selected 29 target genomes.
[2024-01-24 13:50:32,795] [INFO] Target genome list was writen to GCF_000175575.2_ASM17557v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:32,814] [INFO] Task started: fastANI
[2024-01-24 13:50:32,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bda3206-40f5-42bb-816c-7d47973fc08e/GCF_000175575.2_ASM17557v2_genomic.fna.gz --refList GCF_000175575.2_ASM17557v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000175575.2_ASM17557v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:48,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:48,373] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:48,374] [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	100.0	993	994	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
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	77.7761	134	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	77.6422	135	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_003721225.1	s__Acidithiobacillus_B sulfuriphilus	77.5809	181	994	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_018854025.1	s__UBA2486 sp018854025	77.5661	167	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	99.54	99.39	0.91	0.89	6	-
GCA_002341825.1	s__UBA2486 sp002341825	77.556	119	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	77.484	108	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	77.1434	126	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847505.1	s__Acidithiobacillus sp002847505	76.9868	102	994	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	76.9118	105	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	76.7855	53	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	75.97	57	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,375] [INFO] GTDB search result was written to GCF_000175575.2_ASM17557v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:48,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:48,379] [INFO] DFAST_QC result json was written to GCF_000175575.2_ASM17557v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:48,380] [INFO] DFAST_QC completed!
[2024-01-24 13:50:48,380] [INFO] Total running time: 0h1m18s