[2023-06-16 19:07:30,285] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:07:30,288] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:07:30,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference
[2023-06-16 19:07:31,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:07:31,773] [INFO] Task started: Prodigal
[2023-06-16 19:07:31,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0a2f3dc-8ae0-4939-8ad8-92ca646d2b48/GCA_028689175.1_ASM2868917v1_genomic.fna.gz | prodigal -d GCA_028689175.1_ASM2868917v1_genomic.fna/cds.fna -a GCA_028689175.1_ASM2868917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:07:33,332] [INFO] Task succeeded: Prodigal
[2023-06-16 19:07:33,333] [INFO] Task started: HMMsearch
[2023-06-16 19:07:33,333] [INFO] Running command: hmmsearch --tblout GCA_028689175.1_ASM2868917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/reference_markers.hmm GCA_028689175.1_ASM2868917v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:07:33,532] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:07:33,534] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd0a2f3dc-8ae0-4939-8ad8-92ca646d2b48/GCA_028689175.1_ASM2868917v1_genomic.fna.gz]
[2023-06-16 19:07:33,549] [INFO] Query marker FASTA was written to GCA_028689175.1_ASM2868917v1_genomic.fna/markers.fasta
[2023-06-16 19:07:33,549] [INFO] Task started: Blastn
[2023-06-16 19:07:33,550] [INFO] Running command: blastn -query GCA_028689175.1_ASM2868917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/reference_markers.fasta -out GCA_028689175.1_ASM2868917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:07:34,267] [INFO] Task succeeded: Blastn
[2023-06-16 19:07:34,272] [INFO] Selected 15 target genomes.
[2023-06-16 19:07:34,273] [INFO] Target genome list was writen to GCA_028689175.1_ASM2868917v1_genomic.fna/target_genomes.txt
[2023-06-16 19:07:34,279] [INFO] Task started: fastANI
[2023-06-16 19:07:34,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0a2f3dc-8ae0-4939-8ad8-92ca646d2b48/GCA_028689175.1_ASM2868917v1_genomic.fna.gz --refList GCA_028689175.1_ASM2868917v1_genomic.fna/target_genomes.txt --output GCA_028689175.1_ASM2868917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:07:41,039] [INFO] Task succeeded: fastANI
[2023-06-16 19:07:41,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:07:41,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:07:41,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:07:41,041] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:07:41,042] [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
--------------------------------------------------------------------------------
[2023-06-16 19:07:41,044] [INFO] DFAST Taxonomy check result was written to GCA_028689175.1_ASM2868917v1_genomic.fna/tc_result.tsv
[2023-06-16 19:07:41,045] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:07:41,045] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:07:41,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/checkm_data
[2023-06-16 19:07:41,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:07:41,062] [INFO] Task started: CheckM
[2023-06-16 19:07:41,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028689175.1_ASM2868917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028689175.1_ASM2868917v1_genomic.fna/checkm_input GCA_028689175.1_ASM2868917v1_genomic.fna/checkm_result
[2023-06-16 19:07:54,577] [INFO] Task succeeded: CheckM
[2023-06-16 19:07:54,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-16 19:07:54,599] [INFO] ===== Completeness check finished =====
[2023-06-16 19:07:54,600] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:07:54,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028689175.1_ASM2868917v1_genomic.fna/markers.fasta)
[2023-06-16 19:07:54,600] [INFO] Task started: Blastn
[2023-06-16 19:07:54,601] [INFO] Running command: blastn -query GCA_028689175.1_ASM2868917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9f2e3d2-f37e-4a76-b125-09cc8d09b169/dqc_reference/reference_markers_gtdb.fasta -out GCA_028689175.1_ASM2868917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:07:55,413] [INFO] Task succeeded: Blastn
[2023-06-16 19:07:55,417] [INFO] Selected 24 target genomes.
[2023-06-16 19:07:55,418] [INFO] Target genome list was writen to GCA_028689175.1_ASM2868917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:07:55,436] [INFO] Task started: fastANI
[2023-06-16 19:07:55,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0a2f3dc-8ae0-4939-8ad8-92ca646d2b48/GCA_028689175.1_ASM2868917v1_genomic.fna.gz --refList GCA_028689175.1_ASM2868917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028689175.1_ASM2868917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:08:05,294] [INFO] Task succeeded: fastANI
[2023-06-16 19:08:05,296] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 19:08:05,296] [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
--------------------------------------------------------------------------------
[2023-06-16 19:08:05,299] [INFO] GTDB search result was written to GCA_028689175.1_ASM2868917v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:08:05,300] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:08:05,302] [INFO] DFAST_QC result json was written to GCA_028689175.1_ASM2868917v1_genomic.fna/dqc_result.json
[2023-06-16 19:08:05,302] [INFO] DFAST_QC completed!
[2023-06-16 19:08:05,303] [INFO] Total running time: 0h0m35s