[2023-06-29 12:28:54,615] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:28:54,621] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:28:54,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference
[2023-06-29 12:28:55,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:28:55,846] [INFO] Task started: Prodigal
[2023-06-29 12:28:55,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg14264d6b-5e84-45df-ae89-4181ad98b7e4/GCA_021163455.1_ASM2116345v1_genomic.fna.gz | prodigal -d GCA_021163455.1_ASM2116345v1_genomic.fna/cds.fna -a GCA_021163455.1_ASM2116345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:28:58,066] [INFO] Task succeeded: Prodigal
[2023-06-29 12:28:58,066] [INFO] Task started: HMMsearch
[2023-06-29 12:28:58,067] [INFO] Running command: hmmsearch --tblout GCA_021163455.1_ASM2116345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/reference_markers.hmm GCA_021163455.1_ASM2116345v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:28:58,292] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:28:58,293] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg14264d6b-5e84-45df-ae89-4181ad98b7e4/GCA_021163455.1_ASM2116345v1_genomic.fna.gz]
[2023-06-29 12:28:58,312] [INFO] Query marker FASTA was written to GCA_021163455.1_ASM2116345v1_genomic.fna/markers.fasta
[2023-06-29 12:28:58,313] [INFO] Task started: Blastn
[2023-06-29 12:28:58,313] [INFO] Running command: blastn -query GCA_021163455.1_ASM2116345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/reference_markers.fasta -out GCA_021163455.1_ASM2116345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:28:58,866] [INFO] Task succeeded: Blastn
[2023-06-29 12:28:58,870] [INFO] Selected 4 target genomes.
[2023-06-29 12:28:58,870] [INFO] Target genome list was writen to GCA_021163455.1_ASM2116345v1_genomic.fna/target_genomes.txt
[2023-06-29 12:28:58,874] [INFO] Task started: fastANI
[2023-06-29 12:28:58,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg14264d6b-5e84-45df-ae89-4181ad98b7e4/GCA_021163455.1_ASM2116345v1_genomic.fna.gz --refList GCA_021163455.1_ASM2116345v1_genomic.fna/target_genomes.txt --output GCA_021163455.1_ASM2116345v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:29:01,549] [INFO] Task succeeded: fastANI
[2023-06-29 12:29:01,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:29:01,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:29:01,552] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:29:01,553] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:29:01,553] [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 12:29:01,556] [INFO] DFAST Taxonomy check result was written to GCA_021163455.1_ASM2116345v1_genomic.fna/tc_result.tsv
[2023-06-29 12:29:01,557] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:29:01,557] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:29:01,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/checkm_data
[2023-06-29 12:29:01,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:29:01,587] [INFO] Task started: CheckM
[2023-06-29 12:29:01,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021163455.1_ASM2116345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021163455.1_ASM2116345v1_genomic.fna/checkm_input GCA_021163455.1_ASM2116345v1_genomic.fna/checkm_result
[2023-06-29 12:29:17,226] [INFO] Task succeeded: CheckM
[2023-06-29 12:29:17,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 5.82%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-29 12:29:17,251] [INFO] ===== Completeness check finished =====
[2023-06-29 12:29:17,251] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:29:17,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021163455.1_ASM2116345v1_genomic.fna/markers.fasta)
[2023-06-29 12:29:17,252] [INFO] Task started: Blastn
[2023-06-29 12:29:17,252] [INFO] Running command: blastn -query GCA_021163455.1_ASM2116345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c150ac-628d-44fd-898a-6b12cb2f4e06/dqc_reference/reference_markers_gtdb.fasta -out GCA_021163455.1_ASM2116345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:29:17,915] [INFO] Task succeeded: Blastn
[2023-06-29 12:29:17,920] [INFO] Selected 6 target genomes.
[2023-06-29 12:29:17,921] [INFO] Target genome list was writen to GCA_021163455.1_ASM2116345v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:29:17,927] [INFO] Task started: fastANI
[2023-06-29 12:29:17,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg14264d6b-5e84-45df-ae89-4181ad98b7e4/GCA_021163455.1_ASM2116345v1_genomic.fna.gz --refList GCA_021163455.1_ASM2116345v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021163455.1_ASM2116345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:29:20,394] [INFO] Task succeeded: fastANI
[2023-06-29 12:29:20,396] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:29:20,396] [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 12:29:20,400] [INFO] GTDB search result was written to GCA_021163455.1_ASM2116345v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:29:20,400] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:29:20,402] [INFO] DFAST_QC result json was written to GCA_021163455.1_ASM2116345v1_genomic.fna/dqc_result.json
[2023-06-29 12:29:20,403] [INFO] DFAST_QC completed!
[2023-06-29 12:29:20,403] [INFO] Total running time: 0h0m26s