[2024-01-24 14:14:31,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference
[2024-01-24 14:14:32,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,780] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,780] [INFO] Running command: gunzip -c /var/lib/cwl/stge126bbe3-0171-4a64-9e2d-b84f48dd1f39/GCF_001190005.1_ASM119000v1_genomic.fna.gz | prodigal -d GCF_001190005.1_ASM119000v1_genomic.fna/cds.fna -a GCF_001190005.1_ASM119000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:37,721] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:37,722] [INFO] Task started: HMMsearch
[2024-01-24 14:14:37,722] [INFO] Running command: hmmsearch --tblout GCF_001190005.1_ASM119000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/reference_markers.hmm GCF_001190005.1_ASM119000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:37,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:38,001] [INFO] Found 6/6 markers.
[2024-01-24 14:14:38,025] [INFO] Query marker FASTA was written to GCF_001190005.1_ASM119000v1_genomic.fna/markers.fasta
[2024-01-24 14:14:38,026] [INFO] Task started: Blastn
[2024-01-24 14:14:38,026] [INFO] Running command: blastn -query GCF_001190005.1_ASM119000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/reference_markers.fasta -out GCF_001190005.1_ASM119000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:38,632] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:38,636] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:38,637] [INFO] Target genome list was writen to GCF_001190005.1_ASM119000v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:38,685] [INFO] Task started: fastANI
[2024-01-24 14:14:38,685] [INFO] Running command: fastANI --query /var/lib/cwl/stge126bbe3-0171-4a64-9e2d-b84f48dd1f39/GCF_001190005.1_ASM119000v1_genomic.fna.gz --refList GCF_001190005.1_ASM119000v1_genomic.fna/target_genomes.txt --output GCF_001190005.1_ASM119000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:46,132] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:46,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:46,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:46,149] [INFO] Found 16 fastANI hits (15 hits with ANI > threshold)
[2024-01-24 14:14:46,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:46,150] [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
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001190005.1	1050107	1584	suspected-type	True	100.0	630	631	95	conclusive
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001888965.1	1050107	1584	suspected-type	True	99.9952	630	631	95	conclusive
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_001434635.1	29397	1584	suspected-type	True	97.8571	473	631	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_004354615.1	1537158	1584	suspected-type	True	97.7864	515	631	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=NBRC 3202	GCA_006740305.1	83684	1584	suspected-type	True	97.758	548	631	95	conclusive
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_000192165.1	29397	1584	suspected-type	True	97.7217	543	631	95	conclusive
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_001888925.1	1537158	1584	suspected-type	True	97.6743	531	631	95	conclusive
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_002278095.1	29397	1584	type	True	97.5852	542	631	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001433875.1	83684	1584	suspected-type	True	97.3489	481	631	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=NBRC 13953	GCA_006539405.1	1585	1584	type	True	97.2591	487	631	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=DSM 20081	GCA_001437195.1	1585	1584	type	True	97.2103	500	631	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=ATCC 11842	GCA_000056065.1	1585	1584	type	True	97.0858	529	631	95	conclusive
Lactobacillus delbrueckii subsp. indicus	strain=JCM 15610	GCA_001189855.1	249265	1584	type	True	97.0836	502	631	95	conclusive
Lactobacillus delbrueckii subsp. indicus	strain=DSM 15996	GCA_001435795.1	249265	1584	type	True	97.0602	500	631	95	conclusive
Lactobacillus delbrueckii subsp. indicus	strain=JCM 15610	GCA_001908415.1	249265	1584	type	True	96.8501	531	631	95	conclusive
Lactobacillus equicursoris	strain=JCM 14600	GCA_001311765.1	420645	420645	type	True	82.3485	401	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:46,152] [INFO] DFAST Taxonomy check result was written to GCF_001190005.1_ASM119000v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:46,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:46,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:46,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/checkm_data
[2024-01-24 14:14:46,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:46,180] [INFO] Task started: CheckM
[2024-01-24 14:14:46,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001190005.1_ASM119000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001190005.1_ASM119000v1_genomic.fna/checkm_input GCF_001190005.1_ASM119000v1_genomic.fna/checkm_result
[2024-01-24 14:15:07,975] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:07,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:07,997] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:07,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:07,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001190005.1_ASM119000v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:07,998] [INFO] Task started: Blastn
[2024-01-24 14:15:07,998] [INFO] Running command: blastn -query GCF_001190005.1_ASM119000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0a7d67-908f-4976-9992-137a532af975/dqc_reference/reference_markers_gtdb.fasta -out GCF_001190005.1_ASM119000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:08,771] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:08,776] [INFO] Selected 9 target genomes.
[2024-01-24 14:15:08,776] [INFO] Target genome list was writen to GCF_001190005.1_ASM119000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:08,785] [INFO] Task started: fastANI
[2024-01-24 14:15:08,785] [INFO] Running command: fastANI --query /var/lib/cwl/stge126bbe3-0171-4a64-9e2d-b84f48dd1f39/GCF_001190005.1_ASM119000v1_genomic.fna.gz --refList GCF_001190005.1_ASM119000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001190005.1_ASM119000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:12,345] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:12,355] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:12,355] [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_001433875.1	s__Lactobacillus delbrueckii	97.3154	482	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.56	96.59	0.89	0.81	103	conclusive
GCA_004556255.1	s__Lactobacillus delbrueckii_B	94.7847	359	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587775.1	s__Lactobacillus nasalidis	86.9817	365	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.92	99.91	0.92	0.89	3	-
GCF_009695985.1	s__Lactobacillus porci	82.6516	418	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.20	0.91	0.90	4	-
GCF_001434815.1	s__Lactobacillus equicursoris	82.3934	389	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.84	97.67	0.88	0.82	5	-
GCF_000615445.1	s__Lactobacillus hamsteri	78.4824	51	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCA_905214545.1	s__Lactobacillus sp905214545	77.4161	105	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,357] [INFO] GTDB search result was written to GCF_001190005.1_ASM119000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:12,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:12,360] [INFO] DFAST_QC result json was written to GCF_001190005.1_ASM119000v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:12,361] [INFO] DFAST_QC completed!
[2024-01-24 14:15:12,361] [INFO] Total running time: 0h0m41s