[2023-06-29 15:55:32,838] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:55:32,840] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:55:32,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference
[2023-06-29 15:55:34,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:55:34,137] [INFO] Task started: Prodigal
[2023-06-29 15:55:34,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ca5ef54-c897-4623-b8d8-f2ac2283a104/GCA_011049625.1_ASM1104962v1_genomic.fna.gz | prodigal -d GCA_011049625.1_ASM1104962v1_genomic.fna/cds.fna -a GCA_011049625.1_ASM1104962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:55:37,073] [INFO] Task succeeded: Prodigal
[2023-06-29 15:55:37,073] [INFO] Task started: HMMsearch
[2023-06-29 15:55:37,073] [INFO] Running command: hmmsearch --tblout GCA_011049625.1_ASM1104962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/reference_markers.hmm GCA_011049625.1_ASM1104962v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:55:37,245] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:55:37,246] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8ca5ef54-c897-4623-b8d8-f2ac2283a104/GCA_011049625.1_ASM1104962v1_genomic.fna.gz]
[2023-06-29 15:55:37,264] [INFO] Query marker FASTA was written to GCA_011049625.1_ASM1104962v1_genomic.fna/markers.fasta
[2023-06-29 15:55:37,264] [INFO] Task started: Blastn
[2023-06-29 15:55:37,264] [INFO] Running command: blastn -query GCA_011049625.1_ASM1104962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/reference_markers.fasta -out GCA_011049625.1_ASM1104962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:55:37,893] [INFO] Task succeeded: Blastn
[2023-06-29 15:55:37,897] [INFO] Selected 8 target genomes.
[2023-06-29 15:55:37,898] [INFO] Target genome list was writen to GCA_011049625.1_ASM1104962v1_genomic.fna/target_genomes.txt
[2023-06-29 15:55:37,899] [INFO] Task started: fastANI
[2023-06-29 15:55:37,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca5ef54-c897-4623-b8d8-f2ac2283a104/GCA_011049625.1_ASM1104962v1_genomic.fna.gz --refList GCA_011049625.1_ASM1104962v1_genomic.fna/target_genomes.txt --output GCA_011049625.1_ASM1104962v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:55:43,042] [INFO] Task succeeded: fastANI
[2023-06-29 15:55:43,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:55:43,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:55:43,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:55:43,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:55:43,045] [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 15:55:43,047] [INFO] DFAST Taxonomy check result was written to GCA_011049625.1_ASM1104962v1_genomic.fna/tc_result.tsv
[2023-06-29 15:55:43,047] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:55:43,048] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:55:43,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/checkm_data
[2023-06-29 15:55:43,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:55:43,067] [INFO] Task started: CheckM
[2023-06-29 15:55:43,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011049625.1_ASM1104962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011049625.1_ASM1104962v1_genomic.fna/checkm_input GCA_011049625.1_ASM1104962v1_genomic.fna/checkm_result
[2023-06-29 15:55:59,363] [INFO] Task succeeded: CheckM
[2023-06-29 15:55:59,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:55:59,382] [INFO] ===== Completeness check finished =====
[2023-06-29 15:55:59,382] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:55:59,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011049625.1_ASM1104962v1_genomic.fna/markers.fasta)
[2023-06-29 15:55:59,383] [INFO] Task started: Blastn
[2023-06-29 15:55:59,383] [INFO] Running command: blastn -query GCA_011049625.1_ASM1104962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a353514-88dd-4533-9c5d-d0b38267b6c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_011049625.1_ASM1104962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:56:00,067] [INFO] Task succeeded: Blastn
[2023-06-29 15:56:00,072] [INFO] Selected 14 target genomes.
[2023-06-29 15:56:00,072] [INFO] Target genome list was writen to GCA_011049625.1_ASM1104962v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:56:00,079] [INFO] Task started: fastANI
[2023-06-29 15:56:00,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca5ef54-c897-4623-b8d8-f2ac2283a104/GCA_011049625.1_ASM1104962v1_genomic.fna.gz --refList GCA_011049625.1_ASM1104962v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011049625.1_ASM1104962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:56:07,895] [INFO] Task succeeded: fastANI
[2023-06-29 15:56:07,897] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:56:07,898] [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 15:56:07,900] [INFO] GTDB search result was written to GCA_011049625.1_ASM1104962v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:56:07,901] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:56:07,903] [INFO] DFAST_QC result json was written to GCA_011049625.1_ASM1104962v1_genomic.fna/dqc_result.json
[2023-06-29 15:56:07,904] [INFO] DFAST_QC completed!
[2023-06-29 15:56:07,904] [INFO] Total running time: 0h0m35s