[2023-06-29 07:58:18,240] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:58:18,241] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:58:18,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference
[2023-06-29 07:58:20,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:58:20,806] [INFO] Task started: Prodigal
[2023-06-29 07:58:20,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e741c42-860f-47cc-ab75-442b3d35b622/GCA_027339005.1_ASM2733900v1_genomic.fna.gz | prodigal -d GCA_027339005.1_ASM2733900v1_genomic.fna/cds.fna -a GCA_027339005.1_ASM2733900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:58:22,916] [INFO] Task succeeded: Prodigal
[2023-06-29 07:58:22,917] [INFO] Task started: HMMsearch
[2023-06-29 07:58:22,917] [INFO] Running command: hmmsearch --tblout GCA_027339005.1_ASM2733900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/reference_markers.hmm GCA_027339005.1_ASM2733900v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:58:23,141] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:58:23,143] [INFO] Found 6/6 markers.
[2023-06-29 07:58:23,159] [INFO] Query marker FASTA was written to GCA_027339005.1_ASM2733900v1_genomic.fna/markers.fasta
[2023-06-29 07:58:23,159] [INFO] Task started: Blastn
[2023-06-29 07:58:23,160] [INFO] Running command: blastn -query GCA_027339005.1_ASM2733900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/reference_markers.fasta -out GCA_027339005.1_ASM2733900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:25,960] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:25,965] [INFO] Selected 15 target genomes.
[2023-06-29 07:58:25,966] [INFO] Target genome list was writen to GCA_027339005.1_ASM2733900v1_genomic.fna/target_genomes.txt
[2023-06-29 07:58:25,970] [INFO] Task started: fastANI
[2023-06-29 07:58:25,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e741c42-860f-47cc-ab75-442b3d35b622/GCA_027339005.1_ASM2733900v1_genomic.fna.gz --refList GCA_027339005.1_ASM2733900v1_genomic.fna/target_genomes.txt --output GCA_027339005.1_ASM2733900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:58:30,826] [INFO] Task succeeded: fastANI
[2023-06-29 07:58:30,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:58:30,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:58:30,829] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:58:30,830] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 07:58:30,830] [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 07:58:30,832] [INFO] DFAST Taxonomy check result was written to GCA_027339005.1_ASM2733900v1_genomic.fna/tc_result.tsv
[2023-06-29 07:58:30,832] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:58:30,833] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:58:30,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/checkm_data
[2023-06-29 07:58:30,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:58:30,853] [INFO] Task started: CheckM
[2023-06-29 07:58:30,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027339005.1_ASM2733900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027339005.1_ASM2733900v1_genomic.fna/checkm_input GCA_027339005.1_ASM2733900v1_genomic.fna/checkm_result
[2023-06-29 07:58:44,907] [INFO] Task succeeded: CheckM
[2023-06-29 07:58:44,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:58:44,926] [INFO] ===== Completeness check finished =====
[2023-06-29 07:58:44,927] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:58:44,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027339005.1_ASM2733900v1_genomic.fna/markers.fasta)
[2023-06-29 07:58:44,928] [INFO] Task started: Blastn
[2023-06-29 07:58:44,928] [INFO] Running command: blastn -query GCA_027339005.1_ASM2733900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607825e4-89e4-4d0c-93b8-427c9c51d5a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027339005.1_ASM2733900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:45,670] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:45,675] [INFO] Selected 20 target genomes.
[2023-06-29 07:58:45,675] [INFO] Target genome list was writen to GCA_027339005.1_ASM2733900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:58:45,687] [INFO] Task started: fastANI
[2023-06-29 07:58:45,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e741c42-860f-47cc-ab75-442b3d35b622/GCA_027339005.1_ASM2733900v1_genomic.fna.gz --refList GCA_027339005.1_ASM2733900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027339005.1_ASM2733900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:58:51,520] [INFO] Task succeeded: fastANI
[2023-06-29 07:58:51,522] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 07:58:51,522] [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 07:58:51,524] [INFO] GTDB search result was written to GCA_027339005.1_ASM2733900v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:58:51,525] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:58:51,529] [INFO] DFAST_QC result json was written to GCA_027339005.1_ASM2733900v1_genomic.fna/dqc_result.json
[2023-06-29 07:58:51,529] [INFO] DFAST_QC completed!
[2023-06-29 07:58:51,529] [INFO] Total running time: 0h0m33s