[2023-06-27 19:20:47,298] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:20:47,300] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:20:47,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference
[2023-06-27 19:20:50,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:20:50,506] [INFO] Task started: Prodigal
[2023-06-27 19:20:50,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4b35047-bd24-45fe-9ad4-fcd2af90d75c/GCA_002425005.1_ASM242500v1_genomic.fna.gz | prodigal -d GCA_002425005.1_ASM242500v1_genomic.fna/cds.fna -a GCA_002425005.1_ASM242500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:21:05,866] [INFO] Task succeeded: Prodigal
[2023-06-27 19:21:05,867] [INFO] Task started: HMMsearch
[2023-06-27 19:21:05,867] [INFO] Running command: hmmsearch --tblout GCA_002425005.1_ASM242500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/reference_markers.hmm GCA_002425005.1_ASM242500v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:21:06,171] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:21:06,174] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd4b35047-bd24-45fe-9ad4-fcd2af90d75c/GCA_002425005.1_ASM242500v1_genomic.fna.gz]
[2023-06-27 19:21:06,208] [INFO] Query marker FASTA was written to GCA_002425005.1_ASM242500v1_genomic.fna/markers.fasta
[2023-06-27 19:21:06,209] [INFO] Task started: Blastn
[2023-06-27 19:21:06,209] [INFO] Running command: blastn -query GCA_002425005.1_ASM242500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/reference_markers.fasta -out GCA_002425005.1_ASM242500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:21:06,871] [INFO] Task succeeded: Blastn
[2023-06-27 19:21:06,876] [INFO] Selected 24 target genomes.
[2023-06-27 19:21:06,877] [INFO] Target genome list was writen to GCA_002425005.1_ASM242500v1_genomic.fna/target_genomes.txt
[2023-06-27 19:21:06,879] [INFO] Task started: fastANI
[2023-06-27 19:21:06,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b35047-bd24-45fe-9ad4-fcd2af90d75c/GCA_002425005.1_ASM242500v1_genomic.fna.gz --refList GCA_002425005.1_ASM242500v1_genomic.fna/target_genomes.txt --output GCA_002425005.1_ASM242500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:21:24,201] [INFO] Task succeeded: fastANI
[2023-06-27 19:21:24,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:21:24,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:21:24,204] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 19:21:24,204] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 19:21:24,204] [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
--------------------------------------------------------------------------------
[2023-06-27 19:21:24,206] [INFO] DFAST Taxonomy check result was written to GCA_002425005.1_ASM242500v1_genomic.fna/tc_result.tsv
[2023-06-27 19:21:24,207] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:21:24,207] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:21:24,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/checkm_data
[2023-06-27 19:21:24,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:21:24,251] [INFO] Task started: CheckM
[2023-06-27 19:21:24,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002425005.1_ASM242500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002425005.1_ASM242500v1_genomic.fna/checkm_input GCA_002425005.1_ASM242500v1_genomic.fna/checkm_result
[2023-06-27 19:22:11,188] [INFO] Task succeeded: CheckM
[2023-06-27 19:22:11,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:22:11,215] [INFO] ===== Completeness check finished =====
[2023-06-27 19:22:11,216] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:22:11,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002425005.1_ASM242500v1_genomic.fna/markers.fasta)
[2023-06-27 19:22:11,217] [INFO] Task started: Blastn
[2023-06-27 19:22:11,217] [INFO] Running command: blastn -query GCA_002425005.1_ASM242500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1ba558-db49-4202-8a3d-afed8d7704a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_002425005.1_ASM242500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:22:12,184] [INFO] Task succeeded: Blastn
[2023-06-27 19:22:12,190] [INFO] Selected 23 target genomes.
[2023-06-27 19:22:12,191] [INFO] Target genome list was writen to GCA_002425005.1_ASM242500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:22:12,200] [INFO] Task started: fastANI
[2023-06-27 19:22:12,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b35047-bd24-45fe-9ad4-fcd2af90d75c/GCA_002425005.1_ASM242500v1_genomic.fna.gz --refList GCA_002425005.1_ASM242500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002425005.1_ASM242500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:22:26,386] [INFO] Task succeeded: fastANI
[2023-06-27 19:22:26,390] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 19:22:26,391] [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_002351955.1	s__UBA2798 sp002351955	99.8237	937	976	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA2798;g__UBA2798	95.0	99.77	99.48	0.95	0.92	7	conclusive
--------------------------------------------------------------------------------
[2023-06-27 19:22:26,393] [INFO] GTDB search result was written to GCA_002425005.1_ASM242500v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:22:26,394] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:22:26,396] [INFO] DFAST_QC result json was written to GCA_002425005.1_ASM242500v1_genomic.fna/dqc_result.json
[2023-06-27 19:22:26,397] [INFO] DFAST_QC completed!
[2023-06-27 19:22:26,397] [INFO] Total running time: 0h1m39s