[2023-06-27 11:41:28,734] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:41:28,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:41:28,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference
[2023-06-27 11:41:30,064] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:41:30,065] [INFO] Task started: Prodigal
[2023-06-27 11:41:30,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg348d4709-bad9-4816-a36b-4a759e60275d/GCA_026993015.1_ASM2699301v1_genomic.fna.gz | prodigal -d GCA_026993015.1_ASM2699301v1_genomic.fna/cds.fna -a GCA_026993015.1_ASM2699301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:41:35,171] [INFO] Task succeeded: Prodigal
[2023-06-27 11:41:35,171] [INFO] Task started: HMMsearch
[2023-06-27 11:41:35,172] [INFO] Running command: hmmsearch --tblout GCA_026993015.1_ASM2699301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/reference_markers.hmm GCA_026993015.1_ASM2699301v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:41:35,395] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:41:35,396] [INFO] Found 6/6 markers.
[2023-06-27 11:41:35,424] [INFO] Query marker FASTA was written to GCA_026993015.1_ASM2699301v1_genomic.fna/markers.fasta
[2023-06-27 11:41:35,425] [INFO] Task started: Blastn
[2023-06-27 11:41:35,425] [INFO] Running command: blastn -query GCA_026993015.1_ASM2699301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/reference_markers.fasta -out GCA_026993015.1_ASM2699301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:36,031] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:36,036] [INFO] Selected 33 target genomes.
[2023-06-27 11:41:36,036] [INFO] Target genome list was writen to GCA_026993015.1_ASM2699301v1_genomic.fna/target_genomes.txt
[2023-06-27 11:41:36,040] [INFO] Task started: fastANI
[2023-06-27 11:41:36,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg348d4709-bad9-4816-a36b-4a759e60275d/GCA_026993015.1_ASM2699301v1_genomic.fna.gz --refList GCA_026993015.1_ASM2699301v1_genomic.fna/target_genomes.txt --output GCA_026993015.1_ASM2699301v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:41:54,731] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:54,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:41:54,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:41:54,733] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:41:54,733] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:41:54,733] [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
--------------------------------------------------------------------------------
[2023-06-27 11:41:54,736] [INFO] DFAST Taxonomy check result was written to GCA_026993015.1_ASM2699301v1_genomic.fna/tc_result.tsv
[2023-06-27 11:41:54,736] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:41:54,737] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:41:54,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/checkm_data
[2023-06-27 11:41:54,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:41:54,769] [INFO] Task started: CheckM
[2023-06-27 11:41:54,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026993015.1_ASM2699301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026993015.1_ASM2699301v1_genomic.fna/checkm_input GCA_026993015.1_ASM2699301v1_genomic.fna/checkm_result
[2023-06-27 11:42:16,752] [INFO] Task succeeded: CheckM
[2023-06-27 11:42:16,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.18%
Contamintation: 2.98%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-27 11:42:16,781] [INFO] ===== Completeness check finished =====
[2023-06-27 11:42:16,782] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:42:16,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026993015.1_ASM2699301v1_genomic.fna/markers.fasta)
[2023-06-27 11:42:16,783] [INFO] Task started: Blastn
[2023-06-27 11:42:16,783] [INFO] Running command: blastn -query GCA_026993015.1_ASM2699301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119e68bc-66f9-42b4-9eb7-686b2ce49548/dqc_reference/reference_markers_gtdb.fasta -out GCA_026993015.1_ASM2699301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:42:17,437] [INFO] Task succeeded: Blastn
[2023-06-27 11:42:17,442] [INFO] Selected 29 target genomes.
[2023-06-27 11:42:17,442] [INFO] Target genome list was writen to GCA_026993015.1_ASM2699301v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:42:17,452] [INFO] Task started: fastANI
[2023-06-27 11:42:17,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg348d4709-bad9-4816-a36b-4a759e60275d/GCA_026993015.1_ASM2699301v1_genomic.fna.gz --refList GCA_026993015.1_ASM2699301v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026993015.1_ASM2699301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:42:33,030] [INFO] Task succeeded: fastANI
[2023-06-27 11:42:33,033] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:42:33,033] [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_011330835.1	s__HyVt-560 sp011330835	96.8094	57	101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UWMA-0217;f__UWMA-0217;g__HyVt-560	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 11:42:33,035] [INFO] GTDB search result was written to GCA_026993015.1_ASM2699301v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:42:33,036] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:42:33,038] [INFO] DFAST_QC result json was written to GCA_026993015.1_ASM2699301v1_genomic.fna/dqc_result.json
[2023-06-27 11:42:33,038] [INFO] DFAST_QC completed!
[2023-06-27 11:42:33,039] [INFO] Total running time: 0h1m4s