[2023-06-29 12:30:06,624] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:30:06,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:30:06,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference
[2023-06-29 12:30:07,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:30:07,930] [INFO] Task started: Prodigal
[2023-06-29 12:30:07,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgc53206dd-b1c2-4a47-bd96-31a13fca4d2f/GCA_023261045.1_ASM2326104v1_genomic.fna.gz | prodigal -d GCA_023261045.1_ASM2326104v1_genomic.fna/cds.fna -a GCA_023261045.1_ASM2326104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:30:22,031] [INFO] Task succeeded: Prodigal
[2023-06-29 12:30:22,032] [INFO] Task started: HMMsearch
[2023-06-29 12:30:22,032] [INFO] Running command: hmmsearch --tblout GCA_023261045.1_ASM2326104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/reference_markers.hmm GCA_023261045.1_ASM2326104v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:30:22,289] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:30:22,290] [INFO] Found 6/6 markers.
[2023-06-29 12:30:22,321] [INFO] Query marker FASTA was written to GCA_023261045.1_ASM2326104v1_genomic.fna/markers.fasta
[2023-06-29 12:30:22,322] [INFO] Task started: Blastn
[2023-06-29 12:30:22,322] [INFO] Running command: blastn -query GCA_023261045.1_ASM2326104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/reference_markers.fasta -out GCA_023261045.1_ASM2326104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:30:22,888] [INFO] Task succeeded: Blastn
[2023-06-29 12:30:22,892] [INFO] Selected 6 target genomes.
[2023-06-29 12:30:22,892] [INFO] Target genome list was writen to GCA_023261045.1_ASM2326104v1_genomic.fna/target_genomes.txt
[2023-06-29 12:30:22,894] [INFO] Task started: fastANI
[2023-06-29 12:30:22,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53206dd-b1c2-4a47-bd96-31a13fca4d2f/GCA_023261045.1_ASM2326104v1_genomic.fna.gz --refList GCA_023261045.1_ASM2326104v1_genomic.fna/target_genomes.txt --output GCA_023261045.1_ASM2326104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:30:27,227] [INFO] Task succeeded: fastANI
[2023-06-29 12:30:27,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:30:27,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:30:27,231] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:30:27,231] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:30:27,231] [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
--------------------------------------------------------------------------------
[2023-06-29 12:30:27,234] [INFO] DFAST Taxonomy check result was written to GCA_023261045.1_ASM2326104v1_genomic.fna/tc_result.tsv
[2023-06-29 12:30:27,235] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:30:27,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:30:27,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/checkm_data
[2023-06-29 12:30:27,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:30:27,272] [INFO] Task started: CheckM
[2023-06-29 12:30:27,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023261045.1_ASM2326104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023261045.1_ASM2326104v1_genomic.fna/checkm_input GCA_023261045.1_ASM2326104v1_genomic.fna/checkm_result
[2023-06-29 12:31:14,057] [INFO] Task succeeded: CheckM
[2023-06-29 12:31:14,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 4.63%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-29 12:31:14,084] [INFO] ===== Completeness check finished =====
[2023-06-29 12:31:14,085] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:31:14,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023261045.1_ASM2326104v1_genomic.fna/markers.fasta)
[2023-06-29 12:31:14,085] [INFO] Task started: Blastn
[2023-06-29 12:31:14,086] [INFO] Running command: blastn -query GCA_023261045.1_ASM2326104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0704fa-c135-43fd-be1a-34006e3612af/dqc_reference/reference_markers_gtdb.fasta -out GCA_023261045.1_ASM2326104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:31:14,816] [INFO] Task succeeded: Blastn
[2023-06-29 12:31:14,821] [INFO] Selected 19 target genomes.
[2023-06-29 12:31:14,821] [INFO] Target genome list was writen to GCA_023261045.1_ASM2326104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:31:14,840] [INFO] Task started: fastANI
[2023-06-29 12:31:14,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgc53206dd-b1c2-4a47-bd96-31a13fca4d2f/GCA_023261045.1_ASM2326104v1_genomic.fna.gz --refList GCA_023261045.1_ASM2326104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023261045.1_ASM2326104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:31:24,484] [INFO] Task succeeded: fastANI
[2023-06-29 12:31:24,487] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:31:24,487] [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
--------------------------------------------------------------------------------
[2023-06-29 12:31:24,489] [INFO] GTDB search result was written to GCA_023261045.1_ASM2326104v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:31:24,490] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:31:24,492] [INFO] DFAST_QC result json was written to GCA_023261045.1_ASM2326104v1_genomic.fna/dqc_result.json
[2023-06-29 12:31:24,493] [INFO] DFAST_QC completed!
[2023-06-29 12:31:24,493] [INFO] Total running time: 0h1m18s