[2024-01-24 14:30:45,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference
[2024-01-24 14:30:46,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,469] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b8507bb-c240-4bce-bd0e-fd0b7c15cd9b/GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna.gz | prodigal -d GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/cds.fna -a GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:50,246] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:50,246] [INFO] Task started: HMMsearch
[2024-01-24 14:30:50,247] [INFO] Running command: hmmsearch --tblout GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/reference_markers.hmm GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:50,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:50,496] [INFO] Found 6/6 markers.
[2024-01-24 14:30:50,520] [INFO] Query marker FASTA was written to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/markers.fasta
[2024-01-24 14:30:50,520] [INFO] Task started: Blastn
[2024-01-24 14:30:50,520] [INFO] Running command: blastn -query GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/reference_markers.fasta -out GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:51,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:51,129] [INFO] Selected 20 target genomes.
[2024-01-24 14:30:51,130] [INFO] Target genome list was writen to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/target_genomes.txt
[2024-01-24 14:30:51,137] [INFO] Task started: fastANI
[2024-01-24 14:30:51,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8507bb-c240-4bce-bd0e-fd0b7c15cd9b/GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna.gz --refList GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/target_genomes.txt --output GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:58,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:58,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:58,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:58,585] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:58,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:58,585] [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
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	100.0	508	511	95	conclusive
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	81.6979	322	511	95	below_threshold
Limosilactobacillus fermentum	strain=ATCC 14931	GCA_000159215.1	1613	1613	type	True	81.6672	315	511	95	below_threshold
Limosilactobacillus fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	81.5697	327	511	95	below_threshold
Limosilactobacillus equigenerosi	strain=NRIC 0697	GCA_001570685.1	417373	417373	type	True	78.0974	54	511	95	below_threshold
Limosilactobacillus mucosae	strain=DSM 13345	GCA_001436025.1	97478	97478	type	True	78.079	66	511	95	below_threshold
Limosilactobacillus equigenerosi	strain=DSM 18793	GCA_001435245.1	417373	417373	type	True	77.8852	58	511	95	below_threshold
Limosilactobacillus equigenerosi	strain=JCM 14505	GCA_001311375.1	417373	417373	type	True	77.8016	58	511	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	77.3197	70	511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:58,587] [INFO] DFAST Taxonomy check result was written to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/tc_result.tsv
[2024-01-24 14:30:58,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:58,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:58,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/checkm_data
[2024-01-24 14:30:58,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:58,621] [INFO] Task started: CheckM
[2024-01-24 14:30:58,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/checkm_input GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/checkm_result
[2024-01-24 14:31:17,879] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:17,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:17,898] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:17,898] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:17,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/markers.fasta)
[2024-01-24 14:31:17,899] [INFO] Task started: Blastn
[2024-01-24 14:31:17,899] [INFO] Running command: blastn -query GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4f4252-1223-41b3-9ce9-a5f7277b9598/dqc_reference/reference_markers_gtdb.fasta -out GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,695] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,698] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:18,698] [INFO] Target genome list was writen to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:18,714] [INFO] Task started: fastANI
[2024-01-24 14:31:18,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8507bb-c240-4bce-bd0e-fd0b7c15cd9b/GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna.gz --refList GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:25,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:25,735] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:25,735] [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_001293735.1	s__Limosilactobacillus gorillae	100.0	508	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013394085.1	s__Limosilactobacillus fermentum	81.5697	327	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.65	97.32	0.90	0.60	102	-
GCF_000161935.1	s__Limosilactobacillus coleohominis_A	78.6771	51	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843675.1	s__Limosilactobacillus sp012843675	78.209	71	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCF_001436025.1	s__Limosilactobacillus mucosae	78.079	66	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	-
GCF_001434465.1	s__Limosilactobacillus oris	77.8755	75	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCF_001435345.1	s__Limosilactobacillus pontis	77.7619	71	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCA_019118465.1	s__Limosilactobacillus faecipullorum	77.5022	62	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	76.3643	51	511	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:25,737] [INFO] GTDB search result was written to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:25,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:25,740] [INFO] DFAST_QC result json was written to GCF_001293735.1_LgorillaeKZ01T_1.0_genomic.fna/dqc_result.json
[2024-01-24 14:31:25,741] [INFO] DFAST_QC completed!
[2024-01-24 14:31:25,741] [INFO] Total running time: 0h0m41s