[2024-01-24 12:46:35,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,246] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference
[2024-01-24 12:46:36,447] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,448] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgae7f12de-f9cf-443d-ba5f-72d47e5549b0/GCF_000708655.1_MS3_genomic.fna.gz | prodigal -d GCF_000708655.1_MS3_genomic.fna/cds.fna -a GCF_000708655.1_MS3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:40,511] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:40,511] [INFO] Task started: HMMsearch
[2024-01-24 12:46:40,511] [INFO] Running command: hmmsearch --tblout GCF_000708655.1_MS3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/reference_markers.hmm GCF_000708655.1_MS3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:40,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:40,689] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae7f12de-f9cf-443d-ba5f-72d47e5549b0/GCF_000708655.1_MS3_genomic.fna.gz]
[2024-01-24 12:46:40,712] [INFO] Query marker FASTA was written to GCF_000708655.1_MS3_genomic.fna/markers.fasta
[2024-01-24 12:46:40,712] [INFO] Task started: Blastn
[2024-01-24 12:46:40,712] [INFO] Running command: blastn -query GCF_000708655.1_MS3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/reference_markers.fasta -out GCF_000708655.1_MS3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:41,298] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:41,302] [INFO] Selected 12 target genomes.
[2024-01-24 12:46:41,302] [INFO] Target genome list was writen to GCF_000708655.1_MS3_genomic.fna/target_genomes.txt
[2024-01-24 12:46:41,314] [INFO] Task started: fastANI
[2024-01-24 12:46:41,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7f12de-f9cf-443d-ba5f-72d47e5549b0/GCF_000708655.1_MS3_genomic.fna.gz --refList GCF_000708655.1_MS3_genomic.fna/target_genomes.txt --output GCF_000708655.1_MS3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:47,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:47,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:47,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:47,851] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:46:47,851] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:47,851] [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
Carnobacterium jeotgali	strain=MS3	GCA_000708655.1	545534	545534	type	True	100.0	725	728	95	conclusive
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	99.9863	728	728	95	conclusive
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	84.3917	551	728	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	84.1782	548	728	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	83.3719	525	728	95	below_threshold
Carnobacterium pleistocenium	strain=FTR1	GCA_000744285.1	181073	181073	type	True	83.0821	534	728	95	below_threshold
Carnobacterium alterfunditum	strain=pf4	GCA_000744115.1	28230	28230	type	True	83.0636	509	728	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	76.5289	56	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:47,852] [INFO] DFAST Taxonomy check result was written to GCF_000708655.1_MS3_genomic.fna/tc_result.tsv
[2024-01-24 12:46:47,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:47,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:47,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/checkm_data
[2024-01-24 12:46:47,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:47,878] [INFO] Task started: CheckM
[2024-01-24 12:46:47,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000708655.1_MS3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000708655.1_MS3_genomic.fna/checkm_input GCF_000708655.1_MS3_genomic.fna/checkm_result
[2024-01-24 12:47:06,997] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:06,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:07,017] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:07,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:07,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000708655.1_MS3_genomic.fna/markers.fasta)
[2024-01-24 12:47:07,018] [INFO] Task started: Blastn
[2024-01-24 12:47:07,018] [INFO] Running command: blastn -query GCF_000708655.1_MS3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6602c9d-3a64-47bc-b3bb-80ba9cd232c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000708655.1_MS3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:07,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:07,861] [INFO] Selected 6 target genomes.
[2024-01-24 12:47:07,862] [INFO] Target genome list was writen to GCF_000708655.1_MS3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:07,866] [INFO] Task started: fastANI
[2024-01-24 12:47:07,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7f12de-f9cf-443d-ba5f-72d47e5549b0/GCF_000708655.1_MS3_genomic.fna.gz --refList GCF_000708655.1_MS3_genomic.fna/target_genomes_gtdb.txt --output GCF_000708655.1_MS3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:11,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:11,382] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:11,383] [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
GCF_000745125.1	s__Carnobacterium_A jeotgali	99.9863	728	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	conclusive
GCF_000746825.1	s__Carnobacterium_A inhibens	84.3738	552	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
GCF_000195575.1	s__Carnobacterium_A sp000195575	83.7238	555	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102725.1	s__Carnobacterium_A viridans	83.3631	526	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_000744285.1	s__Carnobacterium_A pleistocenium	83.0978	532	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744115.1	s__Carnobacterium_A alterfunditum	83.0634	509	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.24	96.49	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:11,385] [INFO] GTDB search result was written to GCF_000708655.1_MS3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:11,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:11,388] [INFO] DFAST_QC result json was written to GCF_000708655.1_MS3_genomic.fna/dqc_result.json
[2024-01-24 12:47:11,388] [INFO] DFAST_QC completed!
[2024-01-24 12:47:11,388] [INFO] Total running time: 0h0m36s