[2024-01-24 12:28:34,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference
[2024-01-24 12:28:35,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,959] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg24d85581-c802-4902-92bc-0d8e3eb4a8c8/GCF_002847505.1_ASM284750v1_genomic.fna.gz | prodigal -d GCF_002847505.1_ASM284750v1_genomic.fna/cds.fna -a GCF_002847505.1_ASM284750v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:44,662] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:44,663] [INFO] Task started: HMMsearch
[2024-01-24 12:28:44,663] [INFO] Running command: hmmsearch --tblout GCF_002847505.1_ASM284750v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/reference_markers.hmm GCF_002847505.1_ASM284750v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:44,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:44,915] [INFO] Found 6/6 markers.
[2024-01-24 12:28:44,948] [INFO] Query marker FASTA was written to GCF_002847505.1_ASM284750v1_genomic.fna/markers.fasta
[2024-01-24 12:28:44,948] [INFO] Task started: Blastn
[2024-01-24 12:28:44,948] [INFO] Running command: blastn -query GCF_002847505.1_ASM284750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/reference_markers.fasta -out GCF_002847505.1_ASM284750v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:45,612] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:45,618] [INFO] Selected 18 target genomes.
[2024-01-24 12:28:45,618] [INFO] Target genome list was writen to GCF_002847505.1_ASM284750v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:45,668] [INFO] Task started: fastANI
[2024-01-24 12:28:45,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg24d85581-c802-4902-92bc-0d8e3eb4a8c8/GCF_002847505.1_ASM284750v1_genomic.fna.gz --refList GCF_002847505.1_ASM284750v1_genomic.fna/target_genomes.txt --output GCF_002847505.1_ASM284750v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:54,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:54,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:54,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:54,657] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:28:54,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:28:54,658] [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 thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	81.1852	522	934	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	81.1721	487	934	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	80.7242	486	934	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	78.4384	239	934	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	77.8139	242	934	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	77.4945	204	934	95	below_threshold
Acidithiobacillus caldus	strain=KU	GCA_018853545.1	33059	33059	type	True	76.5872	107	934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:54,659] [INFO] DFAST Taxonomy check result was written to GCF_002847505.1_ASM284750v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:54,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:54,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:54,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/checkm_data
[2024-01-24 12:28:54,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:54,698] [INFO] Task started: CheckM
[2024-01-24 12:28:54,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002847505.1_ASM284750v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002847505.1_ASM284750v1_genomic.fna/checkm_input GCF_002847505.1_ASM284750v1_genomic.fna/checkm_result
[2024-01-24 12:29:25,344] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:25,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:25,367] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:25,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:25,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002847505.1_ASM284750v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:25,368] [INFO] Task started: Blastn
[2024-01-24 12:29:25,368] [INFO] Running command: blastn -query GCF_002847505.1_ASM284750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2000fbce-fea3-4b93-bbeb-285b19b53936/dqc_reference/reference_markers_gtdb.fasta -out GCF_002847505.1_ASM284750v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:26,421] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:26,425] [INFO] Selected 9 target genomes.
[2024-01-24 12:29:26,426] [INFO] Target genome list was writen to GCF_002847505.1_ASM284750v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:26,437] [INFO] Task started: fastANI
[2024-01-24 12:29:26,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg24d85581-c802-4902-92bc-0d8e3eb4a8c8/GCF_002847505.1_ASM284750v1_genomic.fna.gz --refList GCF_002847505.1_ASM284750v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002847505.1_ASM284750v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:31,967] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:31,974] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:31,974] [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_002847505.1	s__Acidithiobacillus sp002847505	100.0	929	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018853465.1	s__Acidithiobacillus sp018853465	90.3634	654	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	81.1597	486	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
GCF_018853815.1	s__Acidithiobacillus sp018853815	80.8338	491	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015100155.1	s__Acidithiobacillus sp015100155	80.785	512	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_018853445.1	s__Acidithiobacillus sp018853445	80.5541	475	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	77.9701	216	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:31,976] [INFO] GTDB search result was written to GCF_002847505.1_ASM284750v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:31,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:31,981] [INFO] DFAST_QC result json was written to GCF_002847505.1_ASM284750v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:31,981] [INFO] DFAST_QC completed!
[2024-01-24 12:29:31,981] [INFO] Total running time: 0h0m57s