[2023-06-29 00:47:34,107] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:47:34,109] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:47:34,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference
[2023-06-29 00:47:35,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:47:35,361] [INFO] Task started: Prodigal
[2023-06-29 00:47:35,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgb40949df-dd4d-41a1-880a-332c30abae03/GCA_020055965.1_ASM2005596v1_genomic.fna.gz | prodigal -d GCA_020055965.1_ASM2005596v1_genomic.fna/cds.fna -a GCA_020055965.1_ASM2005596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:47:39,782] [INFO] Task succeeded: Prodigal
[2023-06-29 00:47:39,782] [INFO] Task started: HMMsearch
[2023-06-29 00:47:39,782] [INFO] Running command: hmmsearch --tblout GCA_020055965.1_ASM2005596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/reference_markers.hmm GCA_020055965.1_ASM2005596v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:47:39,990] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:47:39,992] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb40949df-dd4d-41a1-880a-332c30abae03/GCA_020055965.1_ASM2005596v1_genomic.fna.gz]
[2023-06-29 00:47:40,015] [INFO] Query marker FASTA was written to GCA_020055965.1_ASM2005596v1_genomic.fna/markers.fasta
[2023-06-29 00:47:40,015] [INFO] Task started: Blastn
[2023-06-29 00:47:40,015] [INFO] Running command: blastn -query GCA_020055965.1_ASM2005596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/reference_markers.fasta -out GCA_020055965.1_ASM2005596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:47:40,494] [INFO] Task succeeded: Blastn
[2023-06-29 00:47:40,498] [INFO] Selected 9 target genomes.
[2023-06-29 00:47:40,498] [INFO] Target genome list was writen to GCA_020055965.1_ASM2005596v1_genomic.fna/target_genomes.txt
[2023-06-29 00:47:40,501] [INFO] Task started: fastANI
[2023-06-29 00:47:40,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgb40949df-dd4d-41a1-880a-332c30abae03/GCA_020055965.1_ASM2005596v1_genomic.fna.gz --refList GCA_020055965.1_ASM2005596v1_genomic.fna/target_genomes.txt --output GCA_020055965.1_ASM2005596v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:47:46,607] [INFO] Task succeeded: fastANI
[2023-06-29 00:47:46,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:47:46,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:47:46,609] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:47:46,610] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:47:46,610] [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 00:47:46,612] [INFO] DFAST Taxonomy check result was written to GCA_020055965.1_ASM2005596v1_genomic.fna/tc_result.tsv
[2023-06-29 00:47:46,614] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:47:46,614] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:47:46,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/checkm_data
[2023-06-29 00:47:46,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:47:46,637] [INFO] Task started: CheckM
[2023-06-29 00:47:46,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020055965.1_ASM2005596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020055965.1_ASM2005596v1_genomic.fna/checkm_input GCA_020055965.1_ASM2005596v1_genomic.fna/checkm_result
[2023-06-29 00:48:07,442] [INFO] Task succeeded: CheckM
[2023-06-29 00:48:07,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.60%
Contamintation: 11.17%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-29 00:48:07,471] [INFO] ===== Completeness check finished =====
[2023-06-29 00:48:07,472] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:48:07,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020055965.1_ASM2005596v1_genomic.fna/markers.fasta)
[2023-06-29 00:48:07,473] [INFO] Task started: Blastn
[2023-06-29 00:48:07,473] [INFO] Running command: blastn -query GCA_020055965.1_ASM2005596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81427ad0-e980-4f82-bfcf-48c1f03c6dd6/dqc_reference/reference_markers_gtdb.fasta -out GCA_020055965.1_ASM2005596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:48:07,909] [INFO] Task succeeded: Blastn
[2023-06-29 00:48:07,915] [INFO] Selected 17 target genomes.
[2023-06-29 00:48:07,915] [INFO] Target genome list was writen to GCA_020055965.1_ASM2005596v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:48:07,924] [INFO] Task started: fastANI
[2023-06-29 00:48:07,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgb40949df-dd4d-41a1-880a-332c30abae03/GCA_020055965.1_ASM2005596v1_genomic.fna.gz --refList GCA_020055965.1_ASM2005596v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020055965.1_ASM2005596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:48:15,514] [INFO] Task succeeded: fastANI
[2023-06-29 00:48:15,516] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:48:15,516] [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 00:48:15,518] [INFO] GTDB search result was written to GCA_020055965.1_ASM2005596v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:48:15,519] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:48:15,521] [INFO] DFAST_QC result json was written to GCA_020055965.1_ASM2005596v1_genomic.fna/dqc_result.json
[2023-06-29 00:48:15,522] [INFO] DFAST_QC completed!
[2023-06-29 00:48:15,522] [INFO] Total running time: 0h0m41s