[2023-06-28 22:24:36,948] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:24:36,951] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:24:36,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference
[2023-06-28 22:24:39,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:24:39,898] [INFO] Task started: Prodigal
[2023-06-28 22:24:39,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg15041138-05bb-4ab8-aa71-966cafd90f91/GCA_020628215.1_ASM2062821v1_genomic.fna.gz | prodigal -d GCA_020628215.1_ASM2062821v1_genomic.fna/cds.fna -a GCA_020628215.1_ASM2062821v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:24:48,056] [INFO] Task succeeded: Prodigal
[2023-06-28 22:24:48,057] [INFO] Task started: HMMsearch
[2023-06-28 22:24:48,057] [INFO] Running command: hmmsearch --tblout GCA_020628215.1_ASM2062821v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/reference_markers.hmm GCA_020628215.1_ASM2062821v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:24:48,213] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:24:48,214] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15041138-05bb-4ab8-aa71-966cafd90f91/GCA_020628215.1_ASM2062821v1_genomic.fna.gz]
[2023-06-28 22:24:48,232] [INFO] Query marker FASTA was written to GCA_020628215.1_ASM2062821v1_genomic.fna/markers.fasta
[2023-06-28 22:24:48,232] [INFO] Task started: Blastn
[2023-06-28 22:24:48,232] [INFO] Running command: blastn -query GCA_020628215.1_ASM2062821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/reference_markers.fasta -out GCA_020628215.1_ASM2062821v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:24:48,818] [INFO] Task succeeded: Blastn
[2023-06-28 22:24:48,822] [INFO] Selected 24 target genomes.
[2023-06-28 22:24:48,823] [INFO] Target genome list was writen to GCA_020628215.1_ASM2062821v1_genomic.fna/target_genomes.txt
[2023-06-28 22:24:48,853] [INFO] Task started: fastANI
[2023-06-28 22:24:48,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg15041138-05bb-4ab8-aa71-966cafd90f91/GCA_020628215.1_ASM2062821v1_genomic.fna.gz --refList GCA_020628215.1_ASM2062821v1_genomic.fna/target_genomes.txt --output GCA_020628215.1_ASM2062821v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:25:03,913] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:03,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:25:03,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:25:03,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:25:03,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 22:25:03,916] [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 22:25:03,918] [INFO] DFAST Taxonomy check result was written to GCA_020628215.1_ASM2062821v1_genomic.fna/tc_result.tsv
[2023-06-28 22:25:03,919] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:25:03,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:25:03,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/checkm_data
[2023-06-28 22:25:03,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:25:03,945] [INFO] Task started: CheckM
[2023-06-28 22:25:03,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020628215.1_ASM2062821v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020628215.1_ASM2062821v1_genomic.fna/checkm_input GCA_020628215.1_ASM2062821v1_genomic.fna/checkm_result
[2023-06-28 22:25:32,287] [INFO] Task succeeded: CheckM
[2023-06-28 22:25:32,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.14%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 22:25:32,305] [INFO] ===== Completeness check finished =====
[2023-06-28 22:25:32,306] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:25:32,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020628215.1_ASM2062821v1_genomic.fna/markers.fasta)
[2023-06-28 22:25:32,306] [INFO] Task started: Blastn
[2023-06-28 22:25:32,306] [INFO] Running command: blastn -query GCA_020628215.1_ASM2062821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a84ce0-1200-49f6-8235-bc7d0a7ffddf/dqc_reference/reference_markers_gtdb.fasta -out GCA_020628215.1_ASM2062821v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:25:33,076] [INFO] Task succeeded: Blastn
[2023-06-28 22:25:33,080] [INFO] Selected 26 target genomes.
[2023-06-28 22:25:33,080] [INFO] Target genome list was writen to GCA_020628215.1_ASM2062821v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:25:33,094] [INFO] Task started: fastANI
[2023-06-28 22:25:33,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg15041138-05bb-4ab8-aa71-966cafd90f91/GCA_020628215.1_ASM2062821v1_genomic.fna.gz --refList GCA_020628215.1_ASM2062821v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020628215.1_ASM2062821v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:25:53,603] [INFO] Task succeeded: fastANI
[2023-06-28 22:25:53,605] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:25:53,605] [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 22:25:53,607] [INFO] GTDB search result was written to GCA_020628215.1_ASM2062821v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:25:53,608] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:25:53,610] [INFO] DFAST_QC result json was written to GCA_020628215.1_ASM2062821v1_genomic.fna/dqc_result.json
[2023-06-28 22:25:53,610] [INFO] DFAST_QC completed!
[2023-06-28 22:25:53,611] [INFO] Total running time: 0h1m17s