[2024-01-24 13:17:04,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference
[2024-01-24 13:17:06,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,206] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg8605d4fd-2a15-40d1-8bb1-272038024fae/GCF_009662475.1_ASM966247v1_genomic.fna.gz | prodigal -d GCF_009662475.1_ASM966247v1_genomic.fna/cds.fna -a GCF_009662475.1_ASM966247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:16,731] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:16,732] [INFO] Task started: HMMsearch
[2024-01-24 13:17:16,732] [INFO] Running command: hmmsearch --tblout GCF_009662475.1_ASM966247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/reference_markers.hmm GCF_009662475.1_ASM966247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:17,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:17,034] [INFO] Found 6/6 markers.
[2024-01-24 13:17:17,069] [INFO] Query marker FASTA was written to GCF_009662475.1_ASM966247v1_genomic.fna/markers.fasta
[2024-01-24 13:17:17,070] [INFO] Task started: Blastn
[2024-01-24 13:17:17,070] [INFO] Running command: blastn -query GCF_009662475.1_ASM966247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/reference_markers.fasta -out GCF_009662475.1_ASM966247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:17,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:17,748] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:17,749] [INFO] Target genome list was writen to GCF_009662475.1_ASM966247v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:17,753] [INFO] Task started: fastANI
[2024-01-24 13:17:17,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg8605d4fd-2a15-40d1-8bb1-272038024fae/GCF_009662475.1_ASM966247v1_genomic.fna.gz --refList GCF_009662475.1_ASM966247v1_genomic.fna/target_genomes.txt --output GCF_009662475.1_ASM966247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:26,870] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:26,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:26,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:26,880] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:17:26,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:26,880] [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_009662475.1	930	930	suspected-type	True	100.0	1137	1138	95	conclusive
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	97.4705	753	1138	95	conclusive
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	97.0463	850	1138	95	conclusive
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	79.9784	263	1138	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	79.7385	256	1138	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	78.0205	187	1138	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	77.8056	184	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:26,882] [INFO] DFAST Taxonomy check result was written to GCF_009662475.1_ASM966247v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:26,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:26,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:26,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/checkm_data
[2024-01-24 13:17:26,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:26,924] [INFO] Task started: CheckM
[2024-01-24 13:17:26,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009662475.1_ASM966247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009662475.1_ASM966247v1_genomic.fna/checkm_input GCF_009662475.1_ASM966247v1_genomic.fna/checkm_result
[2024-01-24 13:18:02,531] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:02,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,554] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:02,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:02,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009662475.1_ASM966247v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:02,555] [INFO] Task started: Blastn
[2024-01-24 13:18:02,555] [INFO] Running command: blastn -query GCF_009662475.1_ASM966247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e8ed57-aa2e-4681-83f6-803976d74e97/dqc_reference/reference_markers_gtdb.fasta -out GCF_009662475.1_ASM966247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,629] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,633] [INFO] Selected 6 target genomes.
[2024-01-24 13:18:03,633] [INFO] Target genome list was writen to GCF_009662475.1_ASM966247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:03,640] [INFO] Task started: fastANI
[2024-01-24 13:18:03,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg8605d4fd-2a15-40d1-8bb1-272038024fae/GCF_009662475.1_ASM966247v1_genomic.fna.gz --refList GCF_009662475.1_ASM966247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009662475.1_ASM966247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:09,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:09,339] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:09,339] [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_009662475.1	s__Acidithiobacillus thiooxidans	100.0	1137	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	conclusive
GCF_015100155.1	s__Acidithiobacillus sp015100155	94.5873	780	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_018853815.1	s__Acidithiobacillus sp018853815	92.8605	771	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853445.1	s__Acidithiobacillus sp018853445	91.7624	684	1138	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	81.3677	512	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853465.1	s__Acidithiobacillus sp018853465	81.1367	493	1138	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,341] [INFO] GTDB search result was written to GCF_009662475.1_ASM966247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:09,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:09,344] [INFO] DFAST_QC result json was written to GCF_009662475.1_ASM966247v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:09,344] [INFO] DFAST_QC completed!
[2024-01-24 13:18:09,344] [INFO] Total running time: 0h1m5s