[2024-01-24 13:28:12,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,783] [INFO] DQC Reference Directory: /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference
[2024-01-24 13:28:14,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,063] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3fa5182-41c8-4827-a5e0-e0b959503f9f/GCF_000423265.1_ASM42326v1_genomic.fna.gz | prodigal -d GCF_000423265.1_ASM42326v1_genomic.fna/cds.fna -a GCF_000423265.1_ASM42326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:17,897] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:17,898] [INFO] Task started: HMMsearch
[2024-01-24 13:28:17,898] [INFO] Running command: hmmsearch --tblout GCF_000423265.1_ASM42326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/reference_markers.hmm GCF_000423265.1_ASM42326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:18,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:18,124] [INFO] Found 6/6 markers.
[2024-01-24 13:28:18,146] [INFO] Query marker FASTA was written to GCF_000423265.1_ASM42326v1_genomic.fna/markers.fasta
[2024-01-24 13:28:18,146] [INFO] Task started: Blastn
[2024-01-24 13:28:18,146] [INFO] Running command: blastn -query GCF_000423265.1_ASM42326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/reference_markers.fasta -out GCF_000423265.1_ASM42326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:18,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:18,786] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:18,787] [INFO] Target genome list was writen to GCF_000423265.1_ASM42326v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:18,889] [INFO] Task started: fastANI
[2024-01-24 13:28:18,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fa5182-41c8-4827-a5e0-e0b959503f9f/GCF_000423265.1_ASM42326v1_genomic.fna.gz --refList GCF_000423265.1_ASM42326v1_genomic.fna/target_genomes.txt --output GCF_000423265.1_ASM42326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:25,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:25,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:25,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:25,637] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:25,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:25,637] [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 saerimneri	strain=DSM 16049	GCA_000423265.1	228229	228229	type	True	100.0	543	547	95	conclusive
Ligilactobacillus saerimneri	strain=DSM 16049	GCA_001435165.1	228229	228229	type	True	99.9302	508	547	95	conclusive
Ligilactobacillus salivarius	strain=ATCC 11741	GCA_000159395.1	1624	1624	type	True	78.303	50	547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:25,640] [INFO] DFAST Taxonomy check result was written to GCF_000423265.1_ASM42326v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:25,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:25,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:25,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/checkm_data
[2024-01-24 13:28:25,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:25,671] [INFO] Task started: CheckM
[2024-01-24 13:28:25,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423265.1_ASM42326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423265.1_ASM42326v1_genomic.fna/checkm_input GCF_000423265.1_ASM42326v1_genomic.fna/checkm_result
[2024-01-24 13:28:45,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:45,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,011] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:46,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:46,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423265.1_ASM42326v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:46,012] [INFO] Task started: Blastn
[2024-01-24 13:28:46,013] [INFO] Running command: blastn -query GCF_000423265.1_ASM42326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge83f610f-c7e8-43df-bd9b-f487869bee82/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423265.1_ASM42326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:46,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:46,764] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:46,764] [INFO] Target genome list was writen to GCF_000423265.1_ASM42326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:46,790] [INFO] Task started: fastANI
[2024-01-24 13:28:46,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fa5182-41c8-4827-a5e0-e0b959503f9f/GCF_000423265.1_ASM42326v1_genomic.fna.gz --refList GCF_000423265.1_ASM42326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423265.1_ASM42326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:54,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:54,394] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:54,394] [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_000423265.1	s__Ligilactobacillus saerimneri	100.0	543	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.58	97.67	0.92	0.88	5	conclusive
GCF_900110005.1	s__Ligilactobacillus ruminis_A	78.1507	50	547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,396] [INFO] GTDB search result was written to GCF_000423265.1_ASM42326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:54,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:54,400] [INFO] DFAST_QC result json was written to GCF_000423265.1_ASM42326v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:54,400] [INFO] DFAST_QC completed!
[2024-01-24 13:28:54,400] [INFO] Total running time: 0h0m42s