[2023-06-13 21:20:32,834] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference
[2023-06-13 21:20:34,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:34,594] [INFO] Task started: Prodigal
[2023-06-13 21:20:34,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f6c5aa9-677d-48ab-be83-9d24e015ea17/GCA_022708745.1_ASM2270874v1_genomic.fna.gz | prodigal -d GCA_022708745.1_ASM2270874v1_genomic.fna/cds.fna -a GCA_022708745.1_ASM2270874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:43,208] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:43,209] [INFO] Task started: HMMsearch
[2023-06-13 21:20:43,209] [INFO] Running command: hmmsearch --tblout GCA_022708745.1_ASM2270874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/reference_markers.hmm GCA_022708745.1_ASM2270874v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:43,425] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:43,427] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0f6c5aa9-677d-48ab-be83-9d24e015ea17/GCA_022708745.1_ASM2270874v1_genomic.fna.gz]
[2023-06-13 21:20:43,450] [INFO] Query marker FASTA was written to GCA_022708745.1_ASM2270874v1_genomic.fna/markers.fasta
[2023-06-13 21:20:43,450] [INFO] Task started: Blastn
[2023-06-13 21:20:43,451] [INFO] Running command: blastn -query GCA_022708745.1_ASM2270874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/reference_markers.fasta -out GCA_022708745.1_ASM2270874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:43,905] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:43,908] [INFO] Selected 16 target genomes.
[2023-06-13 21:20:43,909] [INFO] Target genome list was writen to GCA_022708745.1_ASM2270874v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:43,910] [INFO] Task started: fastANI
[2023-06-13 21:20:43,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f6c5aa9-677d-48ab-be83-9d24e015ea17/GCA_022708745.1_ASM2270874v1_genomic.fna.gz --refList GCA_022708745.1_ASM2270874v1_genomic.fna/target_genomes.txt --output GCA_022708745.1_ASM2270874v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:56,299] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:56,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:56,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:56,301] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:20:56,301] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 21:20:56,301] [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 21:20:56,305] [INFO] DFAST Taxonomy check result was written to GCA_022708745.1_ASM2270874v1_genomic.fna/tc_result.tsv
[2023-06-13 21:20:56,305] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:56,306] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:56,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/checkm_data
[2023-06-13 21:20:56,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:56,341] [INFO] Task started: CheckM
[2023-06-13 21:20:56,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708745.1_ASM2270874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708745.1_ASM2270874v1_genomic.fna/checkm_input GCA_022708745.1_ASM2270874v1_genomic.fna/checkm_result
[2023-06-13 21:21:25,596] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:25,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:25,619] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:25,619] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:25,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708745.1_ASM2270874v1_genomic.fna/markers.fasta)
[2023-06-13 21:21:25,620] [INFO] Task started: Blastn
[2023-06-13 21:21:25,620] [INFO] Running command: blastn -query GCA_022708745.1_ASM2270874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44c12073-c8aa-4e2d-9889-221c10a3377b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708745.1_ASM2270874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:26,048] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:26,051] [INFO] Selected 19 target genomes.
[2023-06-13 21:21:26,051] [INFO] Target genome list was writen to GCA_022708745.1_ASM2270874v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:26,055] [INFO] Task started: fastANI
[2023-06-13 21:21:26,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f6c5aa9-677d-48ab-be83-9d24e015ea17/GCA_022708745.1_ASM2270874v1_genomic.fna.gz --refList GCA_022708745.1_ASM2270874v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708745.1_ASM2270874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:36,938] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:36,941] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:21:36,941] [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_016788065.1	s__JADKJB01 sp016788065	95.0959	438	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__JADKJB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016713525.1	s__JADKJB01 sp016713525	88.5712	426	554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__OLB10;g__JADKJB01	95.0	98.12	97.53	0.88	0.83	9	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:36,943] [INFO] GTDB search result was written to GCA_022708745.1_ASM2270874v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:36,943] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:36,945] [INFO] DFAST_QC result json was written to GCA_022708745.1_ASM2270874v1_genomic.fna/dqc_result.json
[2023-06-13 21:21:36,945] [INFO] DFAST_QC completed!
[2023-06-13 21:21:36,945] [INFO] Total running time: 0h1m4s