[2023-06-28 09:29:20,288] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:29:20,294] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:29:20,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference
[2023-06-28 09:29:22,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:29:22,033] [INFO] Task started: Prodigal
[2023-06-28 09:29:22,033] [INFO] Running command: gunzip -c /var/lib/cwl/stge4529d8f-5381-4709-beef-e517d77a3439/GCA_017396035.1_ASM1739603v1_genomic.fna.gz | prodigal -d GCA_017396035.1_ASM1739603v1_genomic.fna/cds.fna -a GCA_017396035.1_ASM1739603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:29:24,662] [INFO] Task succeeded: Prodigal
[2023-06-28 09:29:24,663] [INFO] Task started: HMMsearch
[2023-06-28 09:29:24,663] [INFO] Running command: hmmsearch --tblout GCA_017396035.1_ASM1739603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/reference_markers.hmm GCA_017396035.1_ASM1739603v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:29:24,880] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:29:24,881] [INFO] Found 6/6 markers.
[2023-06-28 09:29:24,906] [INFO] Query marker FASTA was written to GCA_017396035.1_ASM1739603v1_genomic.fna/markers.fasta
[2023-06-28 09:29:24,906] [INFO] Task started: Blastn
[2023-06-28 09:29:24,906] [INFO] Running command: blastn -query GCA_017396035.1_ASM1739603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/reference_markers.fasta -out GCA_017396035.1_ASM1739603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:29:25,492] [INFO] Task succeeded: Blastn
[2023-06-28 09:29:25,495] [INFO] Selected 15 target genomes.
[2023-06-28 09:29:25,495] [INFO] Target genome list was writen to GCA_017396035.1_ASM1739603v1_genomic.fna/target_genomes.txt
[2023-06-28 09:29:25,500] [INFO] Task started: fastANI
[2023-06-28 09:29:25,500] [INFO] Running command: fastANI --query /var/lib/cwl/stge4529d8f-5381-4709-beef-e517d77a3439/GCA_017396035.1_ASM1739603v1_genomic.fna.gz --refList GCA_017396035.1_ASM1739603v1_genomic.fna/target_genomes.txt --output GCA_017396035.1_ASM1739603v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:29:35,420] [INFO] Task succeeded: fastANI
[2023-06-28 09:29:35,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:29:35,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:29:35,422] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:29:35,423] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 09:29:35,423] [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
--------------------------------------------------------------------------------
[2023-06-28 09:29:35,424] [INFO] DFAST Taxonomy check result was written to GCA_017396035.1_ASM1739603v1_genomic.fna/tc_result.tsv
[2023-06-28 09:29:35,425] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:29:35,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:29:35,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/checkm_data
[2023-06-28 09:29:35,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:29:35,445] [INFO] Task started: CheckM
[2023-06-28 09:29:35,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017396035.1_ASM1739603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017396035.1_ASM1739603v1_genomic.fna/checkm_input GCA_017396035.1_ASM1739603v1_genomic.fna/checkm_result
[2023-06-28 09:29:49,576] [INFO] Task succeeded: CheckM
[2023-06-28 09:29:49,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.30%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:29:49,593] [INFO] ===== Completeness check finished =====
[2023-06-28 09:29:49,593] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:29:49,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017396035.1_ASM1739603v1_genomic.fna/markers.fasta)
[2023-06-28 09:29:49,594] [INFO] Task started: Blastn
[2023-06-28 09:29:49,594] [INFO] Running command: blastn -query GCA_017396035.1_ASM1739603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg093b76d1-d9cc-4c61-a4b3-022b2458146e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017396035.1_ASM1739603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:29:50,350] [INFO] Task succeeded: Blastn
[2023-06-28 09:29:50,353] [INFO] Selected 25 target genomes.
[2023-06-28 09:29:50,353] [INFO] Target genome list was writen to GCA_017396035.1_ASM1739603v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:29:50,362] [INFO] Task started: fastANI
[2023-06-28 09:29:50,362] [INFO] Running command: fastANI --query /var/lib/cwl/stge4529d8f-5381-4709-beef-e517d77a3439/GCA_017396035.1_ASM1739603v1_genomic.fna.gz --refList GCA_017396035.1_ASM1739603v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017396035.1_ASM1739603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:29:58,314] [INFO] Task succeeded: fastANI
[2023-06-28 09:29:58,315] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 09:29:58,315] [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
--------------------------------------------------------------------------------
[2023-06-28 09:29:58,317] [INFO] GTDB search result was written to GCA_017396035.1_ASM1739603v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:29:58,317] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:29:58,319] [INFO] DFAST_QC result json was written to GCA_017396035.1_ASM1739603v1_genomic.fna/dqc_result.json
[2023-06-28 09:29:58,319] [INFO] DFAST_QC completed!
[2023-06-28 09:29:58,319] [INFO] Total running time: 0h0m38s