[2023-06-13 13:31:54,698] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:31:54,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:31:54,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference
[2023-06-13 13:31:56,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:31:56,039] [INFO] Task started: Prodigal
[2023-06-13 13:31:56,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1ec6416-2b14-41c5-8735-e43077b3476c/GCA_022729495.1_ASM2272949v1_genomic.fna.gz | prodigal -d GCA_022729495.1_ASM2272949v1_genomic.fna/cds.fna -a GCA_022729495.1_ASM2272949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:32:02,993] [INFO] Task succeeded: Prodigal
[2023-06-13 13:32:02,993] [INFO] Task started: HMMsearch
[2023-06-13 13:32:02,994] [INFO] Running command: hmmsearch --tblout GCA_022729495.1_ASM2272949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/reference_markers.hmm GCA_022729495.1_ASM2272949v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:32:03,243] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:32:03,244] [INFO] Found 6/6 markers.
[2023-06-13 13:32:03,271] [INFO] Query marker FASTA was written to GCA_022729495.1_ASM2272949v1_genomic.fna/markers.fasta
[2023-06-13 13:32:03,271] [INFO] Task started: Blastn
[2023-06-13 13:32:03,271] [INFO] Running command: blastn -query GCA_022729495.1_ASM2272949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/reference_markers.fasta -out GCA_022729495.1_ASM2272949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:32:03,863] [INFO] Task succeeded: Blastn
[2023-06-13 13:32:03,867] [INFO] Selected 8 target genomes.
[2023-06-13 13:32:03,868] [INFO] Target genome list was writen to GCA_022729495.1_ASM2272949v1_genomic.fna/target_genomes.txt
[2023-06-13 13:32:03,871] [INFO] Task started: fastANI
[2023-06-13 13:32:03,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ec6416-2b14-41c5-8735-e43077b3476c/GCA_022729495.1_ASM2272949v1_genomic.fna.gz --refList GCA_022729495.1_ASM2272949v1_genomic.fna/target_genomes.txt --output GCA_022729495.1_ASM2272949v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:32:06,413] [INFO] Task succeeded: fastANI
[2023-06-13 13:32:06,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:32:06,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:32:06,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:32:06,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:32:06,416] [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
--------------------------------------------------------------------------------
[2023-06-13 13:32:06,419] [INFO] DFAST Taxonomy check result was written to GCA_022729495.1_ASM2272949v1_genomic.fna/tc_result.tsv
[2023-06-13 13:32:06,420] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:32:06,420] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:32:06,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/checkm_data
[2023-06-13 13:32:06,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:32:06,464] [INFO] Task started: CheckM
[2023-06-13 13:32:06,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022729495.1_ASM2272949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022729495.1_ASM2272949v1_genomic.fna/checkm_input GCA_022729495.1_ASM2272949v1_genomic.fna/checkm_result
[2023-06-13 13:32:33,296] [INFO] Task succeeded: CheckM
[2023-06-13 13:32:33,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.80%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:32:33,324] [INFO] ===== Completeness check finished =====
[2023-06-13 13:32:33,324] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:32:33,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022729495.1_ASM2272949v1_genomic.fna/markers.fasta)
[2023-06-13 13:32:33,325] [INFO] Task started: Blastn
[2023-06-13 13:32:33,325] [INFO] Running command: blastn -query GCA_022729495.1_ASM2272949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e225047-429b-48f5-a200-251a234b9e5b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022729495.1_ASM2272949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:32:34,108] [INFO] Task succeeded: Blastn
[2023-06-13 13:32:34,113] [INFO] Selected 19 target genomes.
[2023-06-13 13:32:34,113] [INFO] Target genome list was writen to GCA_022729495.1_ASM2272949v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:32:34,126] [INFO] Task started: fastANI
[2023-06-13 13:32:34,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ec6416-2b14-41c5-8735-e43077b3476c/GCA_022729495.1_ASM2272949v1_genomic.fna.gz --refList GCA_022729495.1_ASM2272949v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022729495.1_ASM2272949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:32:39,974] [INFO] Task succeeded: fastANI
[2023-06-13 13:32:39,979] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:32:39,979] [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
GCA_003498085.1	s__UBA9088 sp003498085	99.6608	341	490	d__Bacteria;p__UBA9089;c__UBA9088;o__UBA9088;f__UBA9088;g__UBA9088	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-13 13:32:39,982] [INFO] GTDB search result was written to GCA_022729495.1_ASM2272949v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:32:39,983] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:32:39,986] [INFO] DFAST_QC result json was written to GCA_022729495.1_ASM2272949v1_genomic.fna/dqc_result.json
[2023-06-13 13:32:39,986] [INFO] DFAST_QC completed!
[2023-06-13 13:32:39,986] [INFO] Total running time: 0h0m45s