[2024-01-24 13:37:13,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference
[2024-01-24 13:37:15,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:15,053] [INFO] Task started: Prodigal
[2024-01-24 13:37:15,054] [INFO] Running command: gunzip -c /var/lib/cwl/stge9a2caca-d670-4303-99c2-920dc3eaa6ce/GCF_009729015.1_ASM972901v1_genomic.fna.gz | prodigal -d GCF_009729015.1_ASM972901v1_genomic.fna/cds.fna -a GCF_009729015.1_ASM972901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:21,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:21,306] [INFO] Task started: HMMsearch
[2024-01-24 13:37:21,307] [INFO] Running command: hmmsearch --tblout GCF_009729015.1_ASM972901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/reference_markers.hmm GCF_009729015.1_ASM972901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:21,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:21,519] [WARNING] Found 1/6 markers. [/var/lib/cwl/stge9a2caca-d670-4303-99c2-920dc3eaa6ce/GCF_009729015.1_ASM972901v1_genomic.fna.gz]
[2024-01-24 13:37:21,542] [INFO] Query marker FASTA was written to GCF_009729015.1_ASM972901v1_genomic.fna/markers.fasta
[2024-01-24 13:37:21,543] [INFO] Task started: Blastn
[2024-01-24 13:37:21,543] [INFO] Running command: blastn -query GCF_009729015.1_ASM972901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/reference_markers.fasta -out GCF_009729015.1_ASM972901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:22,015] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:22,018] [INFO] Selected 3 target genomes.
[2024-01-24 13:37:22,018] [INFO] Target genome list was writen to GCF_009729015.1_ASM972901v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:22,022] [INFO] Task started: fastANI
[2024-01-24 13:37:22,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a2caca-d670-4303-99c2-920dc3eaa6ce/GCF_009729015.1_ASM972901v1_genomic.fna.gz --refList GCF_009729015.1_ASM972901v1_genomic.fna/target_genomes.txt --output GCF_009729015.1_ASM972901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:24,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:24,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:24,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:24,535] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:24,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:24,535] [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
Acidianus ambivalens	strain=LEI 10	GCA_009729015.1	2283	2283	type	True	100.0	750	750	95	conclusive
Acidianus ambivalens	strain=DSM 3772	GCA_009428885.1	2283	2283	type	True	99.9952	746	750	95	conclusive
Acidianus infernus	strain=DSM 3191	GCA_009729545.1	12915	12915	type	True	92.7667	613	750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:24,537] [INFO] DFAST Taxonomy check result was written to GCF_009729015.1_ASM972901v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:24,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:24,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:24,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/checkm_data
[2024-01-24 13:37:24,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:24,591] [INFO] Task started: CheckM
[2024-01-24 13:37:24,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009729015.1_ASM972901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009729015.1_ASM972901v1_genomic.fna/checkm_input GCF_009729015.1_ASM972901v1_genomic.fna/checkm_result
[2024-01-24 13:37:50,305] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:50,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,325] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:50,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:50,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009729015.1_ASM972901v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:50,327] [INFO] Task started: Blastn
[2024-01-24 13:37:50,327] [INFO] Running command: blastn -query GCF_009729015.1_ASM972901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg879a6409-addb-4370-b362-1108ab22cce9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009729015.1_ASM972901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:50,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:50,799] [INFO] Selected 4 target genomes.
[2024-01-24 13:37:50,799] [INFO] Target genome list was writen to GCF_009729015.1_ASM972901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:50,804] [INFO] Task started: fastANI
[2024-01-24 13:37:50,805] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a2caca-d670-4303-99c2-920dc3eaa6ce/GCF_009729015.1_ASM972901v1_genomic.fna.gz --refList GCF_009729015.1_ASM972901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009729015.1_ASM972901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:53,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:53,223] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:53,223] [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_009729015.1	s__Acidianus ambivalens	100.0	750	750	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Acidianus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_003086435.1	s__Acidianus hospitalis	94.9558	344	750	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Acidianus	95.0	97.25	97.25	0.82	0.82	2	-
GCF_009729545.1	s__Acidianus infernus	92.7376	614	750	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Acidianus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,225] [INFO] GTDB search result was written to GCF_009729015.1_ASM972901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:53,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:53,228] [INFO] DFAST_QC result json was written to GCF_009729015.1_ASM972901v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:53,228] [INFO] DFAST_QC completed!
[2024-01-24 13:37:53,228] [INFO] Total running time: 0h0m39s