[2023-06-28 01:59:57,332] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:59:57,337] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:59:57,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference
[2023-06-28 01:59:58,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:59:58,739] [INFO] Task started: Prodigal
[2023-06-28 01:59:58,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f7605f3-f40e-4d20-bc5d-aa26c2a669db/GCA_944320265.1_BRZ_PT_bin10_genomic.fna.gz | prodigal -d GCA_944320265.1_BRZ_PT_bin10_genomic.fna/cds.fna -a GCA_944320265.1_BRZ_PT_bin10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:00:16,345] [INFO] Task succeeded: Prodigal
[2023-06-28 02:00:16,346] [INFO] Task started: HMMsearch
[2023-06-28 02:00:16,346] [INFO] Running command: hmmsearch --tblout GCA_944320265.1_BRZ_PT_bin10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/reference_markers.hmm GCA_944320265.1_BRZ_PT_bin10_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:00:16,640] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:00:16,641] [INFO] Found 6/6 markers.
[2023-06-28 02:00:16,672] [INFO] Query marker FASTA was written to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/markers.fasta
[2023-06-28 02:00:16,672] [INFO] Task started: Blastn
[2023-06-28 02:00:16,673] [INFO] Running command: blastn -query GCA_944320265.1_BRZ_PT_bin10_genomic.fna/markers.fasta -db /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/reference_markers.fasta -out GCA_944320265.1_BRZ_PT_bin10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:00:17,340] [INFO] Task succeeded: Blastn
[2023-06-28 02:00:17,344] [INFO] Selected 23 target genomes.
[2023-06-28 02:00:17,344] [INFO] Target genome list was writen to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/target_genomes.txt
[2023-06-28 02:00:17,350] [INFO] Task started: fastANI
[2023-06-28 02:00:17,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f7605f3-f40e-4d20-bc5d-aa26c2a669db/GCA_944320265.1_BRZ_PT_bin10_genomic.fna.gz --refList GCA_944320265.1_BRZ_PT_bin10_genomic.fna/target_genomes.txt --output GCA_944320265.1_BRZ_PT_bin10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:00:36,772] [INFO] Task succeeded: fastANI
[2023-06-28 02:00:36,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:00:36,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:00:36,775] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:00:36,775] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:00:36,775] [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
--------------------------------------------------------------------------------
[2023-06-28 02:00:36,778] [INFO] DFAST Taxonomy check result was written to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/tc_result.tsv
[2023-06-28 02:00:36,778] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:00:36,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:00:36,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/checkm_data
[2023-06-28 02:00:36,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:00:36,820] [INFO] Task started: CheckM
[2023-06-28 02:00:36,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320265.1_BRZ_PT_bin10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320265.1_BRZ_PT_bin10_genomic.fna/checkm_input GCA_944320265.1_BRZ_PT_bin10_genomic.fna/checkm_result
[2023-06-28 02:01:25,849] [INFO] Task succeeded: CheckM
[2023-06-28 02:01:25,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:01:25,871] [INFO] ===== Completeness check finished =====
[2023-06-28 02:01:25,872] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:01:25,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320265.1_BRZ_PT_bin10_genomic.fna/markers.fasta)
[2023-06-28 02:01:25,872] [INFO] Task started: Blastn
[2023-06-28 02:01:25,872] [INFO] Running command: blastn -query GCA_944320265.1_BRZ_PT_bin10_genomic.fna/markers.fasta -db /var/lib/cwl/stg904f9b54-7c78-4049-a55f-1018d0ca4a7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320265.1_BRZ_PT_bin10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:01:26,651] [INFO] Task succeeded: Blastn
[2023-06-28 02:01:26,656] [INFO] Selected 26 target genomes.
[2023-06-28 02:01:26,656] [INFO] Target genome list was writen to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:01:26,690] [INFO] Task started: fastANI
[2023-06-28 02:01:26,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f7605f3-f40e-4d20-bc5d-aa26c2a669db/GCA_944320265.1_BRZ_PT_bin10_genomic.fna.gz --refList GCA_944320265.1_BRZ_PT_bin10_genomic.fna/target_genomes_gtdb.txt --output GCA_944320265.1_BRZ_PT_bin10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:01:40,628] [INFO] Task succeeded: fastANI
[2023-06-28 02:01:40,640] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:01:40,641] [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_017694335.1	s__Pullibacteroides excrementavium	86.8994	479	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Pullibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578275.1	s__Pullibacteroides sp910578275	77.6963	127	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Pullibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803485.1	s__Pullibacteroides sp014803485	76.9549	74	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Pullibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586395.1	s__Pullibacteroides sp910586395	76.0874	61	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Pullibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:01:40,643] [INFO] GTDB search result was written to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/result_gtdb.tsv
[2023-06-28 02:01:40,644] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:01:40,648] [INFO] DFAST_QC result json was written to GCA_944320265.1_BRZ_PT_bin10_genomic.fna/dqc_result.json
[2023-06-28 02:01:40,648] [INFO] DFAST_QC completed!
[2023-06-28 02:01:40,648] [INFO] Total running time: 0h1m43s