[2024-01-24 13:45:41,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference
[2024-01-24 13:45:42,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,840] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,840] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3a424ce-2739-40c7-a022-bffccf0ef0a5/GCF_000415925.1_Lot_1.0_genomic.fna.gz | prodigal -d GCF_000415925.1_Lot_1.0_genomic.fna/cds.fna -a GCF_000415925.1_Lot_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:48,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:48,839] [INFO] Task started: HMMsearch
[2024-01-24 13:45:48,839] [INFO] Running command: hmmsearch --tblout GCF_000415925.1_Lot_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/reference_markers.hmm GCF_000415925.1_Lot_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:49,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:49,054] [INFO] Found 6/6 markers.
[2024-01-24 13:45:49,080] [INFO] Query marker FASTA was written to GCF_000415925.1_Lot_1.0_genomic.fna/markers.fasta
[2024-01-24 13:45:49,080] [INFO] Task started: Blastn
[2024-01-24 13:45:49,080] [INFO] Running command: blastn -query GCF_000415925.1_Lot_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/reference_markers.fasta -out GCF_000415925.1_Lot_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:49,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:49,683] [INFO] Selected 12 target genomes.
[2024-01-24 13:45:49,684] [INFO] Target genome list was writen to GCF_000415925.1_Lot_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:45:49,768] [INFO] Task started: fastANI
[2024-01-24 13:45:49,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a424ce-2739-40c7-a022-bffccf0ef0a5/GCF_000415925.1_Lot_1.0_genomic.fna.gz --refList GCF_000415925.1_Lot_1.0_genomic.fna/target_genomes.txt --output GCF_000415925.1_Lot_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:45:55,535] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:55,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:45:55,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:45:55,547] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:45:55,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:45:55,548] [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
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	100.0	768	771	95	conclusive
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	99.9983	771	771	95	conclusive
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	99.9031	766	771	95	conclusive
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_018314255.1	1581	1581	type	True	83.6387	546	771	95	below_threshold
Lentilactobacillus buchneri subsp. silagei	strain=SG162	GCA_013167835.1	2737512	1581	type	True	83.6133	554	771	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	83.5531	546	771	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_009495475.1	1581	1581	type	True	83.5504	558	771	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	83.519	489	771	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	79.302	262	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:45:55,549] [INFO] DFAST Taxonomy check result was written to GCF_000415925.1_Lot_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:45:55,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:45:55,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:45:55,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/checkm_data
[2024-01-24 13:45:55,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:45:55,575] [INFO] Task started: CheckM
[2024-01-24 13:45:55,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000415925.1_Lot_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000415925.1_Lot_1.0_genomic.fna/checkm_input GCF_000415925.1_Lot_1.0_genomic.fna/checkm_result
[2024-01-24 13:46:21,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:21,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:21,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:21,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:21,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000415925.1_Lot_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:46:21,661] [INFO] Task started: Blastn
[2024-01-24 13:46:21,661] [INFO] Running command: blastn -query GCF_000415925.1_Lot_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b2e03df-3ae8-473e-b64b-48a9e3eadbbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000415925.1_Lot_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:22,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:22,455] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:22,455] [INFO] Target genome list was writen to GCF_000415925.1_Lot_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:22,461] [INFO] Task started: fastANI
[2024-01-24 13:46:22,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a424ce-2739-40c7-a022-bffccf0ef0a5/GCF_000415925.1_Lot_1.0_genomic.fna.gz --refList GCF_000415925.1_Lot_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000415925.1_Lot_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:27,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:27,163] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:27,163] [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_001434145.1	s__Lentilactobacillus otakiensis	99.9983	771	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	conclusive
GCF_018314255.1	s__Lentilactobacillus buchneri	83.6387	546	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_007989105.1	s__Lentilactobacillus kefiri	83.5531	546	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_001435575.1	s__Lentilactobacillus sunkii	83.4887	570	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	82.5061	506	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	81.8151	479	771	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:27,168] [INFO] GTDB search result was written to GCF_000415925.1_Lot_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:27,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:27,171] [INFO] DFAST_QC result json was written to GCF_000415925.1_Lot_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:46:27,171] [INFO] DFAST_QC completed!
[2024-01-24 13:46:27,171] [INFO] Total running time: 0h0m46s