[2023-06-18 11:02:12,694] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:12,701] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:12,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference
[2023-06-18 11:02:15,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:15,691] [INFO] Task started: Prodigal
[2023-06-18 11:02:15,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8b17c6a-a504-4c72-84ba-2efb05afd82c/GCA_018676775.1_ASM1867677v1_genomic.fna.gz | prodigal -d GCA_018676775.1_ASM1867677v1_genomic.fna/cds.fna -a GCA_018676775.1_ASM1867677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:02:21,711] [INFO] Task succeeded: Prodigal
[2023-06-18 11:02:21,711] [INFO] Task started: HMMsearch
[2023-06-18 11:02:21,711] [INFO] Running command: hmmsearch --tblout GCA_018676775.1_ASM1867677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/reference_markers.hmm GCA_018676775.1_ASM1867677v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:02:22,004] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:02:22,008] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb8b17c6a-a504-4c72-84ba-2efb05afd82c/GCA_018676775.1_ASM1867677v1_genomic.fna.gz]
[2023-06-18 11:02:22,047] [INFO] Query marker FASTA was written to GCA_018676775.1_ASM1867677v1_genomic.fna/markers.fasta
[2023-06-18 11:02:22,048] [INFO] Task started: Blastn
[2023-06-18 11:02:22,048] [INFO] Running command: blastn -query GCA_018676775.1_ASM1867677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/reference_markers.fasta -out GCA_018676775.1_ASM1867677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:02:22,671] [INFO] Task succeeded: Blastn
[2023-06-18 11:02:22,675] [INFO] Selected 26 target genomes.
[2023-06-18 11:02:22,675] [INFO] Target genome list was writen to GCA_018676775.1_ASM1867677v1_genomic.fna/target_genomes.txt
[2023-06-18 11:02:22,682] [INFO] Task started: fastANI
[2023-06-18 11:02:22,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b17c6a-a504-4c72-84ba-2efb05afd82c/GCA_018676775.1_ASM1867677v1_genomic.fna.gz --refList GCA_018676775.1_ASM1867677v1_genomic.fna/target_genomes.txt --output GCA_018676775.1_ASM1867677v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:02:38,758] [INFO] Task succeeded: fastANI
[2023-06-18 11:02:38,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:02:38,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:02:38,761] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:02:38,761] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:02:38,761] [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
--------------------------------------------------------------------------------
[2023-06-18 11:02:38,765] [INFO] DFAST Taxonomy check result was written to GCA_018676775.1_ASM1867677v1_genomic.fna/tc_result.tsv
[2023-06-18 11:02:38,766] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:02:38,766] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:02:38,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/checkm_data
[2023-06-18 11:02:38,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:02:38,806] [INFO] Task started: CheckM
[2023-06-18 11:02:38,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018676775.1_ASM1867677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018676775.1_ASM1867677v1_genomic.fna/checkm_input GCA_018676775.1_ASM1867677v1_genomic.fna/checkm_result
[2023-06-18 11:03:04,815] [INFO] Task succeeded: CheckM
[2023-06-18 11:03:04,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 11:03:04,850] [INFO] ===== Completeness check finished =====
[2023-06-18 11:03:04,851] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:03:04,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018676775.1_ASM1867677v1_genomic.fna/markers.fasta)
[2023-06-18 11:03:04,851] [INFO] Task started: Blastn
[2023-06-18 11:03:04,852] [INFO] Running command: blastn -query GCA_018676775.1_ASM1867677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae7ddf79-f3dc-4afd-b3c1-309e100ba529/dqc_reference/reference_markers_gtdb.fasta -out GCA_018676775.1_ASM1867677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:05,764] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:05,769] [INFO] Selected 25 target genomes.
[2023-06-18 11:03:05,770] [INFO] Target genome list was writen to GCA_018676775.1_ASM1867677v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:03:05,799] [INFO] Task started: fastANI
[2023-06-18 11:03:05,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b17c6a-a504-4c72-84ba-2efb05afd82c/GCA_018676775.1_ASM1867677v1_genomic.fna.gz --refList GCA_018676775.1_ASM1867677v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018676775.1_ASM1867677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:03:20,079] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:20,083] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:03:20,083] [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
GCA_018693105.1	s__JABHLN01 sp018693105	99.5146	785	947	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-7;g__JABHLN01	95.0	99.49	99.35	0.84	0.81	4	conclusive
--------------------------------------------------------------------------------
[2023-06-18 11:03:20,086] [INFO] GTDB search result was written to GCA_018676775.1_ASM1867677v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:03:20,087] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:03:20,090] [INFO] DFAST_QC result json was written to GCA_018676775.1_ASM1867677v1_genomic.fna/dqc_result.json
[2023-06-18 11:03:20,090] [INFO] DFAST_QC completed!
[2023-06-18 11:03:20,090] [INFO] Total running time: 0h1m7s