[2024-01-24 10:57:24,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:24,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:24,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference
[2024-01-24 10:57:26,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:26,105] [INFO] Task started: Prodigal
[2024-01-24 10:57:26,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgd741b320-b9c4-403d-b4f4-c19e00961ae8/GCF_010378095.1_ASM1037809v1_genomic.fna.gz | prodigal -d GCF_010378095.1_ASM1037809v1_genomic.fna/cds.fna -a GCF_010378095.1_ASM1037809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:35,858] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:35,858] [INFO] Task started: HMMsearch
[2024-01-24 10:57:35,858] [INFO] Running command: hmmsearch --tblout GCF_010378095.1_ASM1037809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/reference_markers.hmm GCF_010378095.1_ASM1037809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,136] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,180] [INFO] Query marker FASTA was written to GCF_010378095.1_ASM1037809v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,181] [INFO] Task started: Blastn
[2024-01-24 10:57:36,181] [INFO] Running command: blastn -query GCF_010378095.1_ASM1037809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/reference_markers.fasta -out GCF_010378095.1_ASM1037809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:36,900] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:36,903] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:36,903] [INFO] Target genome list was writen to GCF_010378095.1_ASM1037809v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:36,933] [INFO] Task started: fastANI
[2024-01-24 10:57:36,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgd741b320-b9c4-403d-b4f4-c19e00961ae8/GCF_010378095.1_ASM1037809v1_genomic.fna.gz --refList GCF_010378095.1_ASM1037809v1_genomic.fna/target_genomes.txt --output GCF_010378095.1_ASM1037809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:46,071] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:46,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:46,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:46,080] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:46,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:46,080] [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 ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	100.0	1021	1026	95	conclusive
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	82.2839	483	1026	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	82.0735	436	1026	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	81.837	485	1026	95	below_threshold
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	81.5254	431	1026	95	below_threshold
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	78.5462	233	1026	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	77.9542	177	1026	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	77.7601	197	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:46,082] [INFO] DFAST Taxonomy check result was written to GCF_010378095.1_ASM1037809v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:46,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:46,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:46,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/checkm_data
[2024-01-24 10:57:46,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:46,115] [INFO] Task started: CheckM
[2024-01-24 10:57:46,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010378095.1_ASM1037809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010378095.1_ASM1037809v1_genomic.fna/checkm_input GCF_010378095.1_ASM1037809v1_genomic.fna/checkm_result
[2024-01-24 10:58:19,084] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:19,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:19,104] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:19,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:19,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010378095.1_ASM1037809v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:19,105] [INFO] Task started: Blastn
[2024-01-24 10:58:19,105] [INFO] Running command: blastn -query GCF_010378095.1_ASM1037809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg207fdf9f-f1bb-49a2-b686-b4dabf8b7d58/dqc_reference/reference_markers_gtdb.fasta -out GCF_010378095.1_ASM1037809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:20,362] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:20,366] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:20,366] [INFO] Target genome list was writen to GCF_010378095.1_ASM1037809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:20,373] [INFO] Task started: fastANI
[2024-01-24 10:58:20,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgd741b320-b9c4-403d-b4f4-c19e00961ae8/GCF_010378095.1_ASM1037809v1_genomic.fna.gz --refList GCF_010378095.1_ASM1037809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010378095.1_ASM1037809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:27,374] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:27,381] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:27,381] [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_010378095.1	s__Acidithiobacillus ferrianus	100.0	1022	1026	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_018854495.1	s__Acidithiobacillus ferrooxidans_C	82.3423	445	1026	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	82.3003	485	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_018854775.1	s__Acidithiobacillus ferriphilus	82.0856	435	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.36	97.93	0.81	0.77	8	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	82.0511	535	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	81.809	484	1026	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	78.5762	235	1026	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_009662475.1	s__Acidithiobacillus thiooxidans	77.829	196	1026	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:27,383] [INFO] GTDB search result was written to GCF_010378095.1_ASM1037809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:27,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:27,386] [INFO] DFAST_QC result json was written to GCF_010378095.1_ASM1037809v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:27,386] [INFO] DFAST_QC completed!
[2024-01-24 10:58:27,386] [INFO] Total running time: 0h1m3s