[2023-06-27 15:57:53,058] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:57:53,063] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:57:53,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference
[2023-06-27 15:57:54,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:57:54,162] [INFO] Task started: Prodigal
[2023-06-27 15:57:54,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fde35d0-5a47-42f4-8f1c-84794439514e/GCA_027348975.1_ASM2734897v1_genomic.fna.gz | prodigal -d GCA_027348975.1_ASM2734897v1_genomic.fna/cds.fna -a GCA_027348975.1_ASM2734897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:57:58,231] [INFO] Task succeeded: Prodigal
[2023-06-27 15:57:58,232] [INFO] Task started: HMMsearch
[2023-06-27 15:57:58,232] [INFO] Running command: hmmsearch --tblout GCA_027348975.1_ASM2734897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/reference_markers.hmm GCA_027348975.1_ASM2734897v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:57:58,389] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:57:58,390] [INFO] Found 6/6 markers.
[2023-06-27 15:57:58,402] [INFO] Query marker FASTA was written to GCA_027348975.1_ASM2734897v1_genomic.fna/markers.fasta
[2023-06-27 15:57:58,402] [INFO] Task started: Blastn
[2023-06-27 15:57:58,402] [INFO] Running command: blastn -query GCA_027348975.1_ASM2734897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/reference_markers.fasta -out GCA_027348975.1_ASM2734897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:57:58,921] [INFO] Task succeeded: Blastn
[2023-06-27 15:57:58,924] [INFO] Selected 16 target genomes.
[2023-06-27 15:57:58,924] [INFO] Target genome list was writen to GCA_027348975.1_ASM2734897v1_genomic.fna/target_genomes.txt
[2023-06-27 15:57:58,929] [INFO] Task started: fastANI
[2023-06-27 15:57:58,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fde35d0-5a47-42f4-8f1c-84794439514e/GCA_027348975.1_ASM2734897v1_genomic.fna.gz --refList GCA_027348975.1_ASM2734897v1_genomic.fna/target_genomes.txt --output GCA_027348975.1_ASM2734897v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:58:07,589] [INFO] Task succeeded: fastANI
[2023-06-27 15:58:07,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:58:07,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:58:07,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:58:07,591] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 15:58:07,591] [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 15:58:07,593] [INFO] DFAST Taxonomy check result was written to GCA_027348975.1_ASM2734897v1_genomic.fna/tc_result.tsv
[2023-06-27 15:58:07,593] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:58:07,593] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:58:07,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/checkm_data
[2023-06-27 15:58:07,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:58:07,608] [INFO] Task started: CheckM
[2023-06-27 15:58:07,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027348975.1_ASM2734897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027348975.1_ASM2734897v1_genomic.fna/checkm_input GCA_027348975.1_ASM2734897v1_genomic.fna/checkm_result
[2023-06-27 15:58:25,559] [INFO] Task succeeded: CheckM
[2023-06-27 15:58:25,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 2.90%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-27 15:58:25,580] [INFO] ===== Completeness check finished =====
[2023-06-27 15:58:25,580] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:58:25,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027348975.1_ASM2734897v1_genomic.fna/markers.fasta)
[2023-06-27 15:58:25,583] [INFO] Task started: Blastn
[2023-06-27 15:58:25,583] [INFO] Running command: blastn -query GCA_027348975.1_ASM2734897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66afc16c-76d6-45d4-8e89-937ce9589ec5/dqc_reference/reference_markers_gtdb.fasta -out GCA_027348975.1_ASM2734897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:58:26,336] [INFO] Task succeeded: Blastn
[2023-06-27 15:58:26,339] [INFO] Selected 22 target genomes.
[2023-06-27 15:58:26,340] [INFO] Target genome list was writen to GCA_027348975.1_ASM2734897v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:58:26,348] [INFO] Task started: fastANI
[2023-06-27 15:58:26,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fde35d0-5a47-42f4-8f1c-84794439514e/GCA_027348975.1_ASM2734897v1_genomic.fna.gz --refList GCA_027348975.1_ASM2734897v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027348975.1_ASM2734897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:58:31,382] [INFO] Task succeeded: fastANI
[2023-06-27 15:58:31,383] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:58:31,383] [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
--------------------------------------------------------------------------------
[2023-06-27 15:58:31,385] [INFO] GTDB search result was written to GCA_027348975.1_ASM2734897v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:58:31,386] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:58:31,388] [INFO] DFAST_QC result json was written to GCA_027348975.1_ASM2734897v1_genomic.fna/dqc_result.json
[2023-06-27 15:58:31,388] [INFO] DFAST_QC completed!
[2023-06-27 15:58:31,389] [INFO] Total running time: 0h0m38s