[2024-01-25 17:48:05,767] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference
[2024-01-25 17:48:06,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,934] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c832370-3be0-40e9-87ba-8f17fca78819/GCF_000183405.1_ASM18340v1_genomic.fna.gz | prodigal -d GCF_000183405.1_ASM18340v1_genomic.fna/cds.fna -a GCF_000183405.1_ASM18340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:11,140] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:11,141] [INFO] Task started: HMMsearch
[2024-01-25 17:48:11,141] [INFO] Running command: hmmsearch --tblout GCF_000183405.1_ASM18340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/reference_markers.hmm GCF_000183405.1_ASM18340v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:11,326] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:11,327] [INFO] Found 6/6 markers.
[2024-01-25 17:48:11,348] [INFO] Query marker FASTA was written to GCF_000183405.1_ASM18340v1_genomic.fna/markers.fasta
[2024-01-25 17:48:11,348] [INFO] Task started: Blastn
[2024-01-25 17:48:11,348] [INFO] Running command: blastn -query GCF_000183405.1_ASM18340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/reference_markers.fasta -out GCF_000183405.1_ASM18340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:11,879] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:11,882] [INFO] Selected 10 target genomes.
[2024-01-25 17:48:11,882] [INFO] Target genome list was writen to GCF_000183405.1_ASM18340v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:11,951] [INFO] Task started: fastANI
[2024-01-25 17:48:11,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c832370-3be0-40e9-87ba-8f17fca78819/GCF_000183405.1_ASM18340v1_genomic.fna.gz --refList GCF_000183405.1_ASM18340v1_genomic.fna/target_genomes.txt --output GCF_000183405.1_ASM18340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:16,413] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:16,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:16,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:16,418] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:16,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:16,418] [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
Calditerrivibrio nitroreducens	strain=DSM 19672	GCA_000183405.1	477976	477976	type	True	100.0	738	738	95	conclusive
Deferribacter autotrophicus	strain=SL50	GCA_008362905.1	500465	500465	type	True	76.4991	53	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:16,420] [INFO] DFAST Taxonomy check result was written to GCF_000183405.1_ASM18340v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:16,420] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:16,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:16,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/checkm_data
[2024-01-25 17:48:16,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:16,445] [INFO] Task started: CheckM
[2024-01-25 17:48:16,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000183405.1_ASM18340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000183405.1_ASM18340v1_genomic.fna/checkm_input GCF_000183405.1_ASM18340v1_genomic.fna/checkm_result
[2024-01-25 17:48:35,033] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:35,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:35,055] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:35,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:35,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000183405.1_ASM18340v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:35,056] [INFO] Task started: Blastn
[2024-01-25 17:48:35,056] [INFO] Running command: blastn -query GCF_000183405.1_ASM18340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f285854-9cc6-48a1-9b16-ff8c04b90c4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000183405.1_ASM18340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:35,833] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:35,836] [INFO] Selected 17 target genomes.
[2024-01-25 17:48:35,836] [INFO] Target genome list was writen to GCF_000183405.1_ASM18340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:35,854] [INFO] Task started: fastANI
[2024-01-25 17:48:35,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c832370-3be0-40e9-87ba-8f17fca78819/GCF_000183405.1_ASM18340v1_genomic.fna.gz --refList GCF_000183405.1_ASM18340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000183405.1_ASM18340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:43,410] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:43,414] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:43,414] [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_000183405.1	s__Calditerrivibrio nitroreducens	100.0	738	738	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Calditerrivibrionaceae;g__Calditerrivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002878065.1	s__Calditerrivibrio nitroreducens_A	90.5336	415	738	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Calditerrivibrionaceae;g__Calditerrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008362905.1	s__Deferribacter autotrophicus	76.5577	54	738	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Deferribacteraceae;g__Deferribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:43,415] [INFO] GTDB search result was written to GCF_000183405.1_ASM18340v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:43,416] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:43,418] [INFO] DFAST_QC result json was written to GCF_000183405.1_ASM18340v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:43,418] [INFO] DFAST_QC completed!
[2024-01-25 17:48:43,418] [INFO] Total running time: 0h0m38s