[2024-01-24 11:05:34,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference
[2024-01-24 11:05:35,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,746] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d16fbb9-e266-4f4b-9b08-f082df157215/GCF_001434145.1_ASM143414v1_genomic.fna.gz | prodigal -d GCF_001434145.1_ASM143414v1_genomic.fna/cds.fna -a GCF_001434145.1_ASM143414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:41,771] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:41,772] [INFO] Task started: HMMsearch
[2024-01-24 11:05:41,772] [INFO] Running command: hmmsearch --tblout GCF_001434145.1_ASM143414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/reference_markers.hmm GCF_001434145.1_ASM143414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:42,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:42,052] [INFO] Found 6/6 markers.
[2024-01-24 11:05:42,077] [INFO] Query marker FASTA was written to GCF_001434145.1_ASM143414v1_genomic.fna/markers.fasta
[2024-01-24 11:05:42,077] [INFO] Task started: Blastn
[2024-01-24 11:05:42,077] [INFO] Running command: blastn -query GCF_001434145.1_ASM143414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/reference_markers.fasta -out GCF_001434145.1_ASM143414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:42,685] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:42,690] [INFO] Selected 12 target genomes.
[2024-01-24 11:05:42,691] [INFO] Target genome list was writen to GCF_001434145.1_ASM143414v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:42,716] [INFO] Task started: fastANI
[2024-01-24 11:05:42,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d16fbb9-e266-4f4b-9b08-f082df157215/GCF_001434145.1_ASM143414v1_genomic.fna.gz --refList GCF_001434145.1_ASM143414v1_genomic.fna/target_genomes.txt --output GCF_001434145.1_ASM143414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,698] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,713] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:48,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:48,714] [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=DSM 19908	GCA_001434145.1	481720	481720	type	True	100.0	772	774	95	conclusive
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	99.9967	766	774	95	conclusive
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	99.9006	766	774	95	conclusive
Lentilactobacillus buchneri subsp. silagei	strain=SG162	GCA_013167835.1	2737512	1581	type	True	83.7146	532	774	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_009495475.1	1581	1581	type	True	83.515	559	774	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_018314255.1	1581	1581	type	True	83.5046	548	774	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	83.4726	493	774	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	83.4091	544	774	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	79.2888	264	774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,715] [INFO] DFAST Taxonomy check result was written to GCF_001434145.1_ASM143414v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/checkm_data
[2024-01-24 11:05:48,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,745] [INFO] Task started: CheckM
[2024-01-24 11:05:48,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434145.1_ASM143414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434145.1_ASM143414v1_genomic.fna/checkm_input GCF_001434145.1_ASM143414v1_genomic.fna/checkm_result
[2024-01-24 11:06:14,421] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:14,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:14,442] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:14,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:14,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434145.1_ASM143414v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:14,443] [INFO] Task started: Blastn
[2024-01-24 11:06:14,444] [INFO] Running command: blastn -query GCF_001434145.1_ASM143414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg491e633a-3cde-4f4a-a8b3-bdb53f5e78af/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434145.1_ASM143414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:15,372] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:15,376] [INFO] Selected 7 target genomes.
[2024-01-24 11:06:15,377] [INFO] Target genome list was writen to GCF_001434145.1_ASM143414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:15,384] [INFO] Task started: fastANI
[2024-01-24 11:06:15,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d16fbb9-e266-4f4b-9b08-f082df157215/GCF_001434145.1_ASM143414v1_genomic.fna.gz --refList GCF_001434145.1_ASM143414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434145.1_ASM143414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:19,582] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,592] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:19,593] [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	100.0	772	774	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	83.5209	547	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_001435575.1	s__Lentilactobacillus sunkii	83.4538	576	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_007989105.1	s__Lentilactobacillus kefiri	83.4091	544	774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	82.5683	496	774	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	81.8122	482	774	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 11:06:19,594] [INFO] GTDB search result was written to GCF_001434145.1_ASM143414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:19,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:19,598] [INFO] DFAST_QC result json was written to GCF_001434145.1_ASM143414v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:19,598] [INFO] DFAST_QC completed!
[2024-01-24 11:06:19,599] [INFO] Total running time: 0h0m45s