[2024-01-24 12:36:58,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,462] [INFO] DQC Reference Directory: /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference
[2024-01-24 12:36:59,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:00,000] [INFO] Task started: Prodigal
[2024-01-24 12:37:00,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f3684fc-6bcd-440f-a191-aa03a5a31204/GCF_017908595.1_ASM1790859v1_genomic.fna.gz | prodigal -d GCF_017908595.1_ASM1790859v1_genomic.fna/cds.fna -a GCF_017908595.1_ASM1790859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:16,642] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:16,643] [INFO] Task started: HMMsearch
[2024-01-24 12:37:16,643] [INFO] Running command: hmmsearch --tblout GCF_017908595.1_ASM1790859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/reference_markers.hmm GCF_017908595.1_ASM1790859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:16,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:16,914] [INFO] Found 6/6 markers.
[2024-01-24 12:37:16,939] [INFO] Query marker FASTA was written to GCF_017908595.1_ASM1790859v1_genomic.fna/markers.fasta
[2024-01-24 12:37:16,940] [INFO] Task started: Blastn
[2024-01-24 12:37:16,940] [INFO] Running command: blastn -query GCF_017908595.1_ASM1790859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/reference_markers.fasta -out GCF_017908595.1_ASM1790859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:17,572] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:17,575] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:17,576] [INFO] Target genome list was writen to GCF_017908595.1_ASM1790859v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:17,584] [INFO] Task started: fastANI
[2024-01-24 12:37:17,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3684fc-6bcd-440f-a191-aa03a5a31204/GCF_017908595.1_ASM1790859v1_genomic.fna.gz --refList GCF_017908595.1_ASM1790859v1_genomic.fna/target_genomes.txt --output GCF_017908595.1_ASM1790859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:29,450] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:29,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:29,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:29,455] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:29,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:29,456] [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
Rhodothermus bifroesti	strain=ISCAR-7401	GCA_017908595.1	2823335	2823335	type	True	100.0	958	958	95	conclusive
Rhodothermus profundi	strain=DSM 22212	GCA_900142415.1	633813	633813	type	True	77.0796	172	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:29,457] [INFO] DFAST Taxonomy check result was written to GCF_017908595.1_ASM1790859v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:29,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:29,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:29,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/checkm_data
[2024-01-24 12:37:29,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:29,491] [INFO] Task started: CheckM
[2024-01-24 12:37:29,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017908595.1_ASM1790859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017908595.1_ASM1790859v1_genomic.fna/checkm_input GCF_017908595.1_ASM1790859v1_genomic.fna/checkm_result
[2024-01-24 12:38:17,492] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:17,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:17,516] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:17,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:17,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017908595.1_ASM1790859v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:17,518] [INFO] Task started: Blastn
[2024-01-24 12:38:17,518] [INFO] Running command: blastn -query GCF_017908595.1_ASM1790859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1089c34-f5c8-401e-b150-888d71451630/dqc_reference/reference_markers_gtdb.fasta -out GCF_017908595.1_ASM1790859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:18,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:18,565] [INFO] Selected 27 target genomes.
[2024-01-24 12:38:18,565] [INFO] Target genome list was writen to GCF_017908595.1_ASM1790859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:18,589] [INFO] Task started: fastANI
[2024-01-24 12:38:18,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3684fc-6bcd-440f-a191-aa03a5a31204/GCF_017908595.1_ASM1790859v1_genomic.fna.gz --refList GCF_017908595.1_ASM1790859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017908595.1_ASM1790859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:33,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:33,560] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:33,560] [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_017908595.1	s__Rhodothermus sp002898335	100.0	958	958	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	99.70	99.65	0.98	0.96	5	conclusive
GCF_000024845.1	s__Rhodothermus marinus	77.4139	246	958	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	95.50	95.42	0.92	0.91	8	-
GCA_015487635.1	s__Rhodothermus sp015487635	77.3499	202	958	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142415.1	s__Rhodothermus profundi	77.0796	172	958	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:33,562] [INFO] GTDB search result was written to GCF_017908595.1_ASM1790859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:33,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:33,565] [INFO] DFAST_QC result json was written to GCF_017908595.1_ASM1790859v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:33,565] [INFO] DFAST_QC completed!
[2024-01-24 12:38:33,565] [INFO] Total running time: 0h1m35s