[2024-01-24 14:31:01,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:01,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:01,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference
[2024-01-24 14:31:04,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:04,076] [INFO] Task started: Prodigal
[2024-01-24 14:31:04,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgc05f8991-f2e5-4bd2-8d7a-eefbddda10b4/GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/cds.fna -a GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:09,739] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:09,740] [INFO] Task started: HMMsearch
[2024-01-24 14:31:09,740] [INFO] Running command: hmmsearch --tblout GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/reference_markers.hmm GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:10,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:10,024] [INFO] Found 6/6 markers.
[2024-01-24 14:31:10,047] [INFO] Query marker FASTA was written to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:31:10,047] [INFO] Task started: Blastn
[2024-01-24 14:31:10,047] [INFO] Running command: blastn -query GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/reference_markers.fasta -out GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:11,262] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:11,266] [INFO] Selected 14 target genomes.
[2024-01-24 14:31:11,266] [INFO] Target genome list was writen to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:31:11,297] [INFO] Task started: fastANI
[2024-01-24 14:31:11,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05f8991-f2e5-4bd2-8d7a-eefbddda10b4/GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna.gz --refList GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:18,150] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:18,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:18,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:18,158] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:31:18,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:18,158] [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
Ligilactobacillus ruminis	strain=DSM 20403	GCA_900113455.1	1623	1623	type	True	100.0	640	649	95	conclusive
Ligilactobacillus ruminis	strain=DSM 20403	GCA_001436475.1	1623	1623	type	True	99.9107	595	649	95	conclusive
Ligilactobacillus ruminis	strain=ATCC 27780	GCA_001008755.1	1623	1623	type	True	99.8979	606	649	95	conclusive
Ligilactobacillus ruminis	strain=NBRC 102161	GCA_001591905.1	1623	1623	type	True	99.8595	574	649	95	conclusive
Ligilactobacillus agilis	strain=DSM 20509	GCA_001436215.1	1601	1601	type	True	79.2906	50	649	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	79.1407	61	649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:18,160] [INFO] DFAST Taxonomy check result was written to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:31:18,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:18,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:18,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/checkm_data
[2024-01-24 14:31:18,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:18,190] [INFO] Task started: CheckM
[2024-01-24 14:31:18,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/checkm_input GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:31:42,736] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:42,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,761] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:42,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:42,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:31:42,762] [INFO] Task started: Blastn
[2024-01-24 14:31:42,762] [INFO] Running command: blastn -query GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg84b4fb8b-41e5-47eb-ab11-8ca4cfe111fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,561] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,565] [INFO] Selected 26 target genomes.
[2024-01-24 14:31:43,565] [INFO] Target genome list was writen to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,583] [INFO] Task started: fastANI
[2024-01-24 14:31:43,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05f8991-f2e5-4bd2-8d7a-eefbddda10b4/GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna.gz --refList GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:55,511] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:55,518] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:55,518] [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_900113455.1	s__Ligilactobacillus ruminis	100.0	640	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.28	96.58	0.88	0.79	57	conclusive
GCF_900110005.1	s__Ligilactobacillus ruminis_A	80.3239	130	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCF_001434535.1	s__Ligilactobacillus animalis	79.7091	57	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCF_001436215.1	s__Ligilactobacillus agilis	79.2906	50	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.37	95.88	0.84	0.79	29	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	78.991	58	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	78.4364	50	649	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:55,520] [INFO] GTDB search result was written to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:55,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:55,524] [INFO] DFAST_QC result json was written to GCF_900113455.1_IMG-taxon_2593339155_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:31:55,524] [INFO] DFAST_QC completed!
[2024-01-24 14:31:55,524] [INFO] Total running time: 0h0m54s