[2023-06-28 23:39:51,668] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:51,670] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:51,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference
[2023-06-28 23:39:52,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:52,971] [INFO] Task started: Prodigal
[2023-06-28 23:39:52,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg06dc18e2-0d5d-4b67-835a-859d69561f38/GCA_944341895.1_BRZ_DR_bin56_genomic.fna.gz | prodigal -d GCA_944341895.1_BRZ_DR_bin56_genomic.fna/cds.fna -a GCA_944341895.1_BRZ_DR_bin56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:39:57,229] [INFO] Task succeeded: Prodigal
[2023-06-28 23:39:57,229] [INFO] Task started: HMMsearch
[2023-06-28 23:39:57,229] [INFO] Running command: hmmsearch --tblout GCA_944341895.1_BRZ_DR_bin56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/reference_markers.hmm GCA_944341895.1_BRZ_DR_bin56_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:39:57,462] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:39:57,463] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg06dc18e2-0d5d-4b67-835a-859d69561f38/GCA_944341895.1_BRZ_DR_bin56_genomic.fna.gz]
[2023-06-28 23:39:57,481] [INFO] Query marker FASTA was written to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/markers.fasta
[2023-06-28 23:39:57,482] [INFO] Task started: Blastn
[2023-06-28 23:39:57,482] [INFO] Running command: blastn -query GCA_944341895.1_BRZ_DR_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/reference_markers.fasta -out GCA_944341895.1_BRZ_DR_bin56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:39:58,107] [INFO] Task succeeded: Blastn
[2023-06-28 23:39:58,112] [INFO] Selected 16 target genomes.
[2023-06-28 23:39:58,112] [INFO] Target genome list was writen to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/target_genomes.txt
[2023-06-28 23:39:58,115] [INFO] Task started: fastANI
[2023-06-28 23:39:58,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg06dc18e2-0d5d-4b67-835a-859d69561f38/GCA_944341895.1_BRZ_DR_bin56_genomic.fna.gz --refList GCA_944341895.1_BRZ_DR_bin56_genomic.fna/target_genomes.txt --output GCA_944341895.1_BRZ_DR_bin56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:40:08,602] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:08,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:40:08,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:40:08,605] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:40:08,605] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:40:08,605] [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 23:40:08,607] [INFO] DFAST Taxonomy check result was written to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/tc_result.tsv
[2023-06-28 23:40:08,608] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:40:08,608] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:40:08,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/checkm_data
[2023-06-28 23:40:08,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:40:08,628] [INFO] Task started: CheckM
[2023-06-28 23:40:08,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944341895.1_BRZ_DR_bin56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944341895.1_BRZ_DR_bin56_genomic.fna/checkm_input GCA_944341895.1_BRZ_DR_bin56_genomic.fna/checkm_result
[2023-06-28 23:40:28,257] [INFO] Task succeeded: CheckM
[2023-06-28 23:40:28,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:40:28,276] [INFO] ===== Completeness check finished =====
[2023-06-28 23:40:28,277] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:40:28,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944341895.1_BRZ_DR_bin56_genomic.fna/markers.fasta)
[2023-06-28 23:40:28,277] [INFO] Task started: Blastn
[2023-06-28 23:40:28,278] [INFO] Running command: blastn -query GCA_944341895.1_BRZ_DR_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a2d5343-ae18-4add-83ee-cdc89c6001ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_944341895.1_BRZ_DR_bin56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:29,135] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:29,140] [INFO] Selected 15 target genomes.
[2023-06-28 23:40:29,140] [INFO] Target genome list was writen to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:40:29,149] [INFO] Task started: fastANI
[2023-06-28 23:40:29,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg06dc18e2-0d5d-4b67-835a-859d69561f38/GCA_944341895.1_BRZ_DR_bin56_genomic.fna.gz --refList GCA_944341895.1_BRZ_DR_bin56_genomic.fna/target_genomes_gtdb.txt --output GCA_944341895.1_BRZ_DR_bin56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:40:33,708] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:33,722] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:40:33,723] [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_017886545.1	s__Borkfalkia sp017886545	81.0327	235	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761665.1	s__Borkfalkia avicola	80.7495	209	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.39	98.30	0.86	0.81	7	-
GCA_019114625.1	s__Borkfalkia faecigallinarum	80.5934	200	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.33	98.33	0.78	0.78	2	-
GCA_017886895.1	s__Borkfalkia sp017886895	80.4096	214	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115565.1	s__Borkfalkia excrementipullorum	79.9511	199	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.67	99.67	0.86	0.86	2	-
GCA_019114245.1	s__Borkfalkia faecipullorum	79.7401	198	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.25	98.23	0.86	0.84	3	-
GCA_019115995.1	s__Borkfalkia avistercoris	79.5176	168	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.93	99.93	0.94	0.94	2	-
GCA_904419945.1	s__Borkfalkia sp904419945	79.1446	170	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134775.1	s__Borkfalkia ceftriaxoniphila	78.5806	169	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.18	98.64	0.97	0.95	4	-
GCF_904391375.1	s__Gallimonas faecavium	76.5053	79	458	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:40:33,725] [INFO] GTDB search result was written to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/result_gtdb.tsv
[2023-06-28 23:40:33,727] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:40:33,731] [INFO] DFAST_QC result json was written to GCA_944341895.1_BRZ_DR_bin56_genomic.fna/dqc_result.json
[2023-06-28 23:40:33,731] [INFO] DFAST_QC completed!
[2023-06-28 23:40:33,731] [INFO] Total running time: 0h0m42s