[2023-06-29 00:23:37,511] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:23:37,513] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:23:37,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference
[2023-06-29 00:23:38,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:23:38,721] [INFO] Task started: Prodigal
[2023-06-29 00:23:38,721] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb48369f-2b5d-4f77-b209-658e8f90b9ab/GCA_020346705.1_ASM2034670v1_genomic.fna.gz | prodigal -d GCA_020346705.1_ASM2034670v1_genomic.fna/cds.fna -a GCA_020346705.1_ASM2034670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:23:47,533] [INFO] Task succeeded: Prodigal
[2023-06-29 00:23:47,534] [INFO] Task started: HMMsearch
[2023-06-29 00:23:47,534] [INFO] Running command: hmmsearch --tblout GCA_020346705.1_ASM2034670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/reference_markers.hmm GCA_020346705.1_ASM2034670v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:23:47,792] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:23:47,796] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb48369f-2b5d-4f77-b209-658e8f90b9ab/GCA_020346705.1_ASM2034670v1_genomic.fna.gz]
[2023-06-29 00:23:47,835] [INFO] Query marker FASTA was written to GCA_020346705.1_ASM2034670v1_genomic.fna/markers.fasta
[2023-06-29 00:23:47,836] [INFO] Task started: Blastn
[2023-06-29 00:23:47,836] [INFO] Running command: blastn -query GCA_020346705.1_ASM2034670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/reference_markers.fasta -out GCA_020346705.1_ASM2034670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:48,404] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:48,408] [INFO] Selected 10 target genomes.
[2023-06-29 00:23:48,409] [INFO] Target genome list was writen to GCA_020346705.1_ASM2034670v1_genomic.fna/target_genomes.txt
[2023-06-29 00:23:48,414] [INFO] Task started: fastANI
[2023-06-29 00:23:48,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb48369f-2b5d-4f77-b209-658e8f90b9ab/GCA_020346705.1_ASM2034670v1_genomic.fna.gz --refList GCA_020346705.1_ASM2034670v1_genomic.fna/target_genomes.txt --output GCA_020346705.1_ASM2034670v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:23:59,885] [INFO] Task succeeded: fastANI
[2023-06-29 00:23:59,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:23:59,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:23:59,891] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:23:59,891] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:23:59,892] [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 00:23:59,894] [INFO] DFAST Taxonomy check result was written to GCA_020346705.1_ASM2034670v1_genomic.fna/tc_result.tsv
[2023-06-29 00:23:59,895] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:23:59,895] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:23:59,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/checkm_data
[2023-06-29 00:23:59,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:23:59,937] [INFO] Task started: CheckM
[2023-06-29 00:23:59,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020346705.1_ASM2034670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020346705.1_ASM2034670v1_genomic.fna/checkm_input GCA_020346705.1_ASM2034670v1_genomic.fna/checkm_result
[2023-06-29 00:24:29,707] [INFO] Task succeeded: CheckM
[2023-06-29 00:24:29,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:24:29,738] [INFO] ===== Completeness check finished =====
[2023-06-29 00:24:29,739] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:24:29,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020346705.1_ASM2034670v1_genomic.fna/markers.fasta)
[2023-06-29 00:24:29,740] [INFO] Task started: Blastn
[2023-06-29 00:24:29,740] [INFO] Running command: blastn -query GCA_020346705.1_ASM2034670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg308a15a6-7e3d-4380-a46f-11db1f797a75/dqc_reference/reference_markers_gtdb.fasta -out GCA_020346705.1_ASM2034670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:24:30,468] [INFO] Task succeeded: Blastn
[2023-06-29 00:24:30,473] [INFO] Selected 19 target genomes.
[2023-06-29 00:24:30,473] [INFO] Target genome list was writen to GCA_020346705.1_ASM2034670v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:24:30,502] [INFO] Task started: fastANI
[2023-06-29 00:24:30,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb48369f-2b5d-4f77-b209-658e8f90b9ab/GCA_020346705.1_ASM2034670v1_genomic.fna.gz --refList GCA_020346705.1_ASM2034670v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020346705.1_ASM2034670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:24:40,322] [INFO] Task succeeded: fastANI
[2023-06-29 00:24:40,325] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:24:40,325] [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 00:24:40,327] [INFO] GTDB search result was written to GCA_020346705.1_ASM2034670v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:24:40,328] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:24:40,330] [INFO] DFAST_QC result json was written to GCA_020346705.1_ASM2034670v1_genomic.fna/dqc_result.json
[2023-06-29 00:24:40,331] [INFO] DFAST_QC completed!
[2023-06-29 00:24:40,331] [INFO] Total running time: 0h1m3s