[2024-01-24 11:34:41,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,431] [INFO] DQC Reference Directory: /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference
[2024-01-24 11:34:42,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,859] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg18722dac-6074-42d6-9828-77d1b8ef170a/GCF_001591905.1_ASM159190v1_genomic.fna.gz | prodigal -d GCF_001591905.1_ASM159190v1_genomic.fna/cds.fna -a GCF_001591905.1_ASM159190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:47,855] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:47,856] [INFO] Task started: HMMsearch
[2024-01-24 11:34:47,856] [INFO] Running command: hmmsearch --tblout GCF_001591905.1_ASM159190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/reference_markers.hmm GCF_001591905.1_ASM159190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:48,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:48,144] [INFO] Found 6/6 markers.
[2024-01-24 11:34:48,174] [INFO] Query marker FASTA was written to GCF_001591905.1_ASM159190v1_genomic.fna/markers.fasta
[2024-01-24 11:34:48,174] [INFO] Task started: Blastn
[2024-01-24 11:34:48,174] [INFO] Running command: blastn -query GCF_001591905.1_ASM159190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/reference_markers.fasta -out GCF_001591905.1_ASM159190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:48,815] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:48,818] [INFO] Selected 14 target genomes.
[2024-01-24 11:34:48,818] [INFO] Target genome list was writen to GCF_001591905.1_ASM159190v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:49,209] [INFO] Task started: fastANI
[2024-01-24 11:34:49,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg18722dac-6074-42d6-9828-77d1b8ef170a/GCF_001591905.1_ASM159190v1_genomic.fna.gz --refList GCF_001591905.1_ASM159190v1_genomic.fna/target_genomes.txt --output GCF_001591905.1_ASM159190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:54,770] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:54,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:54,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:54,777] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:34:54,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:54,777] [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=NBRC 102161	GCA_001591905.1	1623	1623	type	True	100.0	593	599	95	conclusive
Ligilactobacillus ruminis	strain=ATCC 27780	GCA_001008755.1	1623	1623	type	True	99.9963	588	599	95	conclusive
Ligilactobacillus ruminis	strain=DSM 20403	GCA_900113455.1	1623	1623	type	True	99.991	596	599	95	conclusive
Ligilactobacillus ruminis	strain=DSM 20403	GCA_001436475.1	1623	1623	type	True	99.9907	586	599	95	conclusive
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	78.9949	59	599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:54,779] [INFO] DFAST Taxonomy check result was written to GCF_001591905.1_ASM159190v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:54,779] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:54,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:54,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/checkm_data
[2024-01-24 11:34:54,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:54,803] [INFO] Task started: CheckM
[2024-01-24 11:34:54,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591905.1_ASM159190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591905.1_ASM159190v1_genomic.fna/checkm_input GCF_001591905.1_ASM159190v1_genomic.fna/checkm_result
[2024-01-24 11:35:17,298] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:17,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:17,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:17,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:17,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591905.1_ASM159190v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:17,316] [INFO] Task started: Blastn
[2024-01-24 11:35:17,316] [INFO] Running command: blastn -query GCF_001591905.1_ASM159190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3db2e45-7cc4-447c-a924-e9c5b5b13ea9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591905.1_ASM159190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:18,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:18,164] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:18,164] [INFO] Target genome list was writen to GCF_001591905.1_ASM159190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:18,179] [INFO] Task started: fastANI
[2024-01-24 11:35:18,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg18722dac-6074-42d6-9828-77d1b8ef170a/GCF_001591905.1_ASM159190v1_genomic.fna.gz --refList GCF_001591905.1_ASM159190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591905.1_ASM159190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:29,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:29,613] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:29,613] [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	99.991	596	599	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	79.856	125	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	78.5716	55	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434535.1	s__Ligilactobacillus animalis	78.5618	56	599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	77.932	52	599	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 11:35:29,615] [INFO] GTDB search result was written to GCF_001591905.1_ASM159190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:29,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:29,619] [INFO] DFAST_QC result json was written to GCF_001591905.1_ASM159190v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:29,619] [INFO] DFAST_QC completed!
[2024-01-24 11:35:29,619] [INFO] Total running time: 0h0m48s