[2023-06-28 08:21:36,416] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:21:36,418] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:21:36,418] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference
[2023-06-28 08:21:39,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:21:39,859] [INFO] Task started: Prodigal
[2023-06-28 08:21:39,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c70b149-da15-463d-9469-d28ae80a195e/GCA_944384365.1_BRZ_AM_bin65_genomic.fna.gz | prodigal -d GCA_944384365.1_BRZ_AM_bin65_genomic.fna/cds.fna -a GCA_944384365.1_BRZ_AM_bin65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:21:43,591] [INFO] Task succeeded: Prodigal
[2023-06-28 08:21:43,591] [INFO] Task started: HMMsearch
[2023-06-28 08:21:43,591] [INFO] Running command: hmmsearch --tblout GCA_944384365.1_BRZ_AM_bin65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/reference_markers.hmm GCA_944384365.1_BRZ_AM_bin65_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:21:43,827] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:21:43,829] [INFO] Found 6/6 markers.
[2023-06-28 08:21:43,860] [INFO] Query marker FASTA was written to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/markers.fasta
[2023-06-28 08:21:43,860] [INFO] Task started: Blastn
[2023-06-28 08:21:43,860] [INFO] Running command: blastn -query GCA_944384365.1_BRZ_AM_bin65_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/reference_markers.fasta -out GCA_944384365.1_BRZ_AM_bin65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:21:44,877] [INFO] Task succeeded: Blastn
[2023-06-28 08:21:44,882] [INFO] Selected 17 target genomes.
[2023-06-28 08:21:44,882] [INFO] Target genome list was writen to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/target_genomes.txt
[2023-06-28 08:21:44,887] [INFO] Task started: fastANI
[2023-06-28 08:21:44,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c70b149-da15-463d-9469-d28ae80a195e/GCA_944384365.1_BRZ_AM_bin65_genomic.fna.gz --refList GCA_944384365.1_BRZ_AM_bin65_genomic.fna/target_genomes.txt --output GCA_944384365.1_BRZ_AM_bin65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:21:57,268] [INFO] Task succeeded: fastANI
[2023-06-28 08:21:57,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:21:57,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:21:57,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:21:57,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:21:57,271] [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 08:21:57,274] [INFO] DFAST Taxonomy check result was written to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/tc_result.tsv
[2023-06-28 08:21:57,274] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:21:57,274] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:21:57,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/checkm_data
[2023-06-28 08:21:57,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:21:57,308] [INFO] Task started: CheckM
[2023-06-28 08:21:57,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384365.1_BRZ_AM_bin65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384365.1_BRZ_AM_bin65_genomic.fna/checkm_input GCA_944384365.1_BRZ_AM_bin65_genomic.fna/checkm_result
[2023-06-28 08:22:16,256] [INFO] Task succeeded: CheckM
[2023-06-28 08:22:16,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 08:22:16,280] [INFO] ===== Completeness check finished =====
[2023-06-28 08:22:16,280] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:22:16,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384365.1_BRZ_AM_bin65_genomic.fna/markers.fasta)
[2023-06-28 08:22:16,281] [INFO] Task started: Blastn
[2023-06-28 08:22:16,281] [INFO] Running command: blastn -query GCA_944384365.1_BRZ_AM_bin65_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda98c0b-b1b5-458d-959d-1e46dbae0181/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384365.1_BRZ_AM_bin65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:22:17,100] [INFO] Task succeeded: Blastn
[2023-06-28 08:22:17,106] [INFO] Selected 26 target genomes.
[2023-06-28 08:22:17,106] [INFO] Target genome list was writen to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:22:17,123] [INFO] Task started: fastANI
[2023-06-28 08:22:17,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c70b149-da15-463d-9469-d28ae80a195e/GCA_944384365.1_BRZ_AM_bin65_genomic.fna.gz --refList GCA_944384365.1_BRZ_AM_bin65_genomic.fna/target_genomes_gtdb.txt --output GCA_944384365.1_BRZ_AM_bin65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:22:24,980] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:24,989] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:22:24,989] [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_018714045.1	s__Ornithoclostridium faecavium	97.4502	444	573	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA3700;g__Ornithoclostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018716085.1	s__Ornithoclostridium excrementipullorum	77.458	98	573	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA3700;g__Ornithoclostridium	95.0	98.37	98.37	0.93	0.93	2	-
GCF_904382605.1	s__Alloclostridium intestinigallinarum	76.3052	51	573	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA3700;g__Alloclostridium	95.0	97.93	97.77	0.91	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-28 08:22:24,991] [INFO] GTDB search result was written to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/result_gtdb.tsv
[2023-06-28 08:22:24,992] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:22:24,994] [INFO] DFAST_QC result json was written to GCA_944384365.1_BRZ_AM_bin65_genomic.fna/dqc_result.json
[2023-06-28 08:22:24,995] [INFO] DFAST_QC completed!
[2023-06-28 08:22:24,995] [INFO] Total running time: 0h0m49s