[2024-01-24 12:29:19,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:19,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:19,143] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference
[2024-01-24 12:29:20,314] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,315] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,315] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0c4022d-45a6-403e-8753-4d6a51ff5756/GCF_019049135.1_ASM1904913v1_genomic.fna.gz | prodigal -d GCF_019049135.1_ASM1904913v1_genomic.fna/cds.fna -a GCF_019049135.1_ASM1904913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:26,252] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:26,253] [INFO] Task started: HMMsearch
[2024-01-24 12:29:26,253] [INFO] Running command: hmmsearch --tblout GCF_019049135.1_ASM1904913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/reference_markers.hmm GCF_019049135.1_ASM1904913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:26,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:26,494] [INFO] Found 6/6 markers.
[2024-01-24 12:29:26,522] [INFO] Query marker FASTA was written to GCF_019049135.1_ASM1904913v1_genomic.fna/markers.fasta
[2024-01-24 12:29:26,523] [INFO] Task started: Blastn
[2024-01-24 12:29:26,523] [INFO] Running command: blastn -query GCF_019049135.1_ASM1904913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/reference_markers.fasta -out GCF_019049135.1_ASM1904913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:27,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:27,129] [INFO] Selected 19 target genomes.
[2024-01-24 12:29:27,130] [INFO] Target genome list was writen to GCF_019049135.1_ASM1904913v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:27,867] [INFO] Task started: fastANI
[2024-01-24 12:29:27,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0c4022d-45a6-403e-8753-4d6a51ff5756/GCF_019049135.1_ASM1904913v1_genomic.fna.gz --refList GCF_019049135.1_ASM1904913v1_genomic.fna/target_genomes.txt --output GCF_019049135.1_ASM1904913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:36,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:36,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:36,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:36,908] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:36,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:36,908] [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 rapi subsp. rapi	strain=DSM 19907	GCA_001436255.1	2944812	481723	type	True	93.9852	673	811	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	93.9641	664	811	95	below_threshold
Lentilactobacillus kisonensis	strain=DSM 19906	GCA_001434135.1	481722	481722	type	True	81.6441	452	811	95	below_threshold
Lentilactobacillus kisonensis	strain=JCM 15041	GCA_001311425.1	481722	481722	type	True	81.5562	451	811	95	below_threshold
Lentilactobacillus buchneri subsp. silagei	strain=SG162	GCA_013167835.1	2737512	1581	type	True	80.4138	267	811	95	below_threshold
Lentilactobacillus sunkii	strain=DSM 19904	GCA_001435575.1	481719	481719	type	True	80.1259	253	811	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_009495475.1	1581	1581	type	True	79.9419	263	811	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_018314255.1	1581	1581	type	True	79.8774	265	811	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	79.8054	273	811	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	79.7843	273	811	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	79.7748	270	811	95	below_threshold
Lentilactobacillus fungorum	strain=YK48G	GCA_016860605.1	2201250	2201250	type	True	79.7503	373	811	95	below_threshold
Lentilactobacillus parakefiri	strain=JCM 8573	GCA_002157585.1	152332	152332	type	True	79.3437	235	811	95	below_threshold
Lentilactobacillus parakefiri	strain=DSM 10551	GCA_004354625.1	152332	152332	type	True	79.3087	241	811	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	77.7092	55	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:36,910] [INFO] DFAST Taxonomy check result was written to GCF_019049135.1_ASM1904913v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:36,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:36,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:36,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/checkm_data
[2024-01-24 12:29:36,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:36,945] [INFO] Task started: CheckM
[2024-01-24 12:29:36,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019049135.1_ASM1904913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019049135.1_ASM1904913v1_genomic.fna/checkm_input GCF_019049135.1_ASM1904913v1_genomic.fna/checkm_result
[2024-01-24 12:30:01,587] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:01,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:01,614] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:01,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:01,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019049135.1_ASM1904913v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:01,615] [INFO] Task started: Blastn
[2024-01-24 12:30:01,615] [INFO] Running command: blastn -query GCF_019049135.1_ASM1904913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3964c04-1a5b-4e80-8eb4-009b418c9294/dqc_reference/reference_markers_gtdb.fasta -out GCF_019049135.1_ASM1904913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:02,397] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:02,402] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:02,403] [INFO] Target genome list was writen to GCF_019049135.1_ASM1904913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:02,420] [INFO] Task started: fastANI
[2024-01-24 12:30:02,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0c4022d-45a6-403e-8753-4d6a51ff5756/GCF_019049135.1_ASM1904913v1_genomic.fna.gz --refList GCF_019049135.1_ASM1904913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019049135.1_ASM1904913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:09,909] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:09,923] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:09,923] [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_019061365.1	s__Lentilactobacillus sp019061365	99.4559	722	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	conclusive
GCF_001436255.1	s__Lentilactobacillus rapi	93.9852	673	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	81.6649	451	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_001435575.1	s__Lentilactobacillus sunkii	80.1708	251	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_018314255.1	s__Lentilactobacillus buchneri	79.9018	262	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	79.8638	270	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	79.7311	374	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000583655.1	s__Lentilactobacillus farraginis	79.5948	184	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	79.2772	238	811	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,925] [INFO] GTDB search result was written to GCF_019049135.1_ASM1904913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:09,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:09,929] [INFO] DFAST_QC result json was written to GCF_019049135.1_ASM1904913v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:09,929] [INFO] DFAST_QC completed!
[2024-01-24 12:30:09,929] [INFO] Total running time: 0h0m51s