[2023-06-27 15:41:27,296] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:41:27,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:41:27,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference
[2023-06-27 15:41:29,177] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:41:29,178] [INFO] Task started: Prodigal
[2023-06-27 15:41:29,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg9accaa17-cc15-4e2d-b643-c9674fb53358/GCA_026419615.1_ASM2641961v1_genomic.fna.gz | prodigal -d GCA_026419615.1_ASM2641961v1_genomic.fna/cds.fna -a GCA_026419615.1_ASM2641961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:41:31,862] [INFO] Task succeeded: Prodigal
[2023-06-27 15:41:31,863] [INFO] Task started: HMMsearch
[2023-06-27 15:41:31,863] [INFO] Running command: hmmsearch --tblout GCA_026419615.1_ASM2641961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/reference_markers.hmm GCA_026419615.1_ASM2641961v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:41:32,026] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:41:32,027] [INFO] Found 6/6 markers.
[2023-06-27 15:41:32,049] [INFO] Query marker FASTA was written to GCA_026419615.1_ASM2641961v1_genomic.fna/markers.fasta
[2023-06-27 15:41:32,049] [INFO] Task started: Blastn
[2023-06-27 15:41:32,049] [INFO] Running command: blastn -query GCA_026419615.1_ASM2641961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/reference_markers.fasta -out GCA_026419615.1_ASM2641961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:41:32,974] [INFO] Task succeeded: Blastn
[2023-06-27 15:41:32,978] [INFO] Selected 6 target genomes.
[2023-06-27 15:41:32,978] [INFO] Target genome list was writen to GCA_026419615.1_ASM2641961v1_genomic.fna/target_genomes.txt
[2023-06-27 15:41:32,998] [INFO] Task started: fastANI
[2023-06-27 15:41:32,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg9accaa17-cc15-4e2d-b643-c9674fb53358/GCA_026419615.1_ASM2641961v1_genomic.fna.gz --refList GCA_026419615.1_ASM2641961v1_genomic.fna/target_genomes.txt --output GCA_026419615.1_ASM2641961v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:41:36,241] [INFO] Task succeeded: fastANI
[2023-06-27 15:41:36,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:41:36,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:41:36,245] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:41:36,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:41:36,246] [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
Caldimicrobium thiodismutans	strain=TF1	GCA_001548275.1	1653476	1653476	type	True	76.2758	60	468	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:41:36,248] [INFO] DFAST Taxonomy check result was written to GCA_026419615.1_ASM2641961v1_genomic.fna/tc_result.tsv
[2023-06-27 15:41:36,248] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:41:36,248] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:41:36,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/checkm_data
[2023-06-27 15:41:36,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:41:36,266] [INFO] Task started: CheckM
[2023-06-27 15:41:36,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026419615.1_ASM2641961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026419615.1_ASM2641961v1_genomic.fna/checkm_input GCA_026419615.1_ASM2641961v1_genomic.fna/checkm_result
[2023-06-27 15:41:51,300] [INFO] Task succeeded: CheckM
[2023-06-27 15:41:51,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:41:51,320] [INFO] ===== Completeness check finished =====
[2023-06-27 15:41:51,320] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:41:51,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026419615.1_ASM2641961v1_genomic.fna/markers.fasta)
[2023-06-27 15:41:51,321] [INFO] Task started: Blastn
[2023-06-27 15:41:51,321] [INFO] Running command: blastn -query GCA_026419615.1_ASM2641961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47b99cf4-82b3-4bae-8712-f474c360716f/dqc_reference/reference_markers_gtdb.fasta -out GCA_026419615.1_ASM2641961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:41:52,048] [INFO] Task succeeded: Blastn
[2023-06-27 15:41:52,056] [INFO] Selected 17 target genomes.
[2023-06-27 15:41:52,056] [INFO] Target genome list was writen to GCA_026419615.1_ASM2641961v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:41:52,066] [INFO] Task started: fastANI
[2023-06-27 15:41:52,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg9accaa17-cc15-4e2d-b643-c9674fb53358/GCA_026419615.1_ASM2641961v1_genomic.fna.gz --refList GCA_026419615.1_ASM2641961v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026419615.1_ASM2641961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:41:57,610] [INFO] Task succeeded: fastANI
[2023-06-27 15:41:57,614] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:41:57,614] [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_001548275.1	s__Caldimicrobium thiodismutans	76.2758	60	468	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Caldimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 15:41:57,616] [INFO] GTDB search result was written to GCA_026419615.1_ASM2641961v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:41:57,616] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:41:57,634] [INFO] DFAST_QC result json was written to GCA_026419615.1_ASM2641961v1_genomic.fna/dqc_result.json
[2023-06-27 15:41:57,635] [INFO] DFAST_QC completed!
[2023-06-27 15:41:57,635] [INFO] Total running time: 0h0m30s