[2023-06-30 04:49:46,704] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:49:46,713] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:49:46,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference
[2023-06-30 04:49:48,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:49:48,330] [INFO] Task started: Prodigal
[2023-06-30 04:49:48,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg1684e663-f4b0-4210-bc3e-51f4ba909763/GCA_016234155.1_ASM1623415v1_genomic.fna.gz | prodigal -d GCA_016234155.1_ASM1623415v1_genomic.fna/cds.fna -a GCA_016234155.1_ASM1623415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:49:51,769] [INFO] Task succeeded: Prodigal
[2023-06-30 04:49:51,769] [INFO] Task started: HMMsearch
[2023-06-30 04:49:51,769] [INFO] Running command: hmmsearch --tblout GCA_016234155.1_ASM1623415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/reference_markers.hmm GCA_016234155.1_ASM1623415v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:49:51,915] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:49:51,916] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1684e663-f4b0-4210-bc3e-51f4ba909763/GCA_016234155.1_ASM1623415v1_genomic.fna.gz]
[2023-06-30 04:49:51,935] [INFO] Query marker FASTA was written to GCA_016234155.1_ASM1623415v1_genomic.fna/markers.fasta
[2023-06-30 04:49:51,936] [INFO] Task started: Blastn
[2023-06-30 04:49:51,936] [INFO] Running command: blastn -query GCA_016234155.1_ASM1623415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/reference_markers.fasta -out GCA_016234155.1_ASM1623415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:49:52,505] [INFO] Task succeeded: Blastn
[2023-06-30 04:49:52,509] [INFO] Selected 10 target genomes.
[2023-06-30 04:49:52,509] [INFO] Target genome list was writen to GCA_016234155.1_ASM1623415v1_genomic.fna/target_genomes.txt
[2023-06-30 04:49:52,511] [INFO] Task started: fastANI
[2023-06-30 04:49:52,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg1684e663-f4b0-4210-bc3e-51f4ba909763/GCA_016234155.1_ASM1623415v1_genomic.fna.gz --refList GCA_016234155.1_ASM1623415v1_genomic.fna/target_genomes.txt --output GCA_016234155.1_ASM1623415v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:49:57,908] [INFO] Task succeeded: fastANI
[2023-06-30 04:49:57,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:49:57,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:49:57,925] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:49:57,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:49:57,926] [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
--------------------------------------------------------------------------------
[2023-06-30 04:49:57,928] [INFO] DFAST Taxonomy check result was written to GCA_016234155.1_ASM1623415v1_genomic.fna/tc_result.tsv
[2023-06-30 04:49:57,928] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:49:57,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:49:57,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/checkm_data
[2023-06-30 04:49:57,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:49:57,951] [INFO] Task started: CheckM
[2023-06-30 04:49:57,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016234155.1_ASM1623415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016234155.1_ASM1623415v1_genomic.fna/checkm_input GCA_016234155.1_ASM1623415v1_genomic.fna/checkm_result
[2023-06-30 04:50:13,954] [INFO] Task succeeded: CheckM
[2023-06-30 04:50:13,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:50:13,972] [INFO] ===== Completeness check finished =====
[2023-06-30 04:50:13,972] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:50:13,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016234155.1_ASM1623415v1_genomic.fna/markers.fasta)
[2023-06-30 04:50:13,972] [INFO] Task started: Blastn
[2023-06-30 04:50:13,973] [INFO] Running command: blastn -query GCA_016234155.1_ASM1623415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d5901d-5f30-40f6-a3c2-28beb4879870/dqc_reference/reference_markers_gtdb.fasta -out GCA_016234155.1_ASM1623415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:50:14,756] [INFO] Task succeeded: Blastn
[2023-06-30 04:50:14,759] [INFO] Selected 13 target genomes.
[2023-06-30 04:50:14,759] [INFO] Target genome list was writen to GCA_016234155.1_ASM1623415v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:50:14,764] [INFO] Task started: fastANI
[2023-06-30 04:50:14,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg1684e663-f4b0-4210-bc3e-51f4ba909763/GCA_016234155.1_ASM1623415v1_genomic.fna.gz --refList GCA_016234155.1_ASM1623415v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016234155.1_ASM1623415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:50:22,184] [INFO] Task succeeded: fastANI
[2023-06-30 04:50:22,189] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:50:22,189] [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_016234155.1	s__JACRGZ01 sp016234155	100.0	438	451	d__Bacteria;p__Nitrospirota;c__9FT-COMBO-42-15;o__HDB-SIOI813;f__HDB-SIOI813;g__JACRGZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016214375.1	s__JACRHF01 sp016214375	77.1825	55	451	d__Bacteria;p__Nitrospirota;c__9FT-COMBO-42-15;o__HDB-SIOI813;f__HDB-SIOI813;g__JACRHF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001805165.1	s__RBG-16-43-11 sp001805165	76.7411	76	451	d__Bacteria;p__Nitrospirota;c__9FT-COMBO-42-15;o__HDB-SIOI813;f__HDB-SIOI813;g__RBG-16-43-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212215.1	s__JACRGV01 sp016212215	76.0781	62	451	d__Bacteria;p__Nitrospirota;c__9FT-COMBO-42-15;o__HDB-SIOI813;f__HDB-SIOI813;g__JACRGV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:50:22,193] [INFO] GTDB search result was written to GCA_016234155.1_ASM1623415v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:50:22,193] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:50:22,195] [INFO] DFAST_QC result json was written to GCA_016234155.1_ASM1623415v1_genomic.fna/dqc_result.json
[2023-06-30 04:50:22,195] [INFO] DFAST_QC completed!
[2023-06-30 04:50:22,196] [INFO] Total running time: 0h0m35s