[2024-01-24 13:49:00,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference
[2024-01-24 13:49:01,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,585] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,585] [INFO] Running command: gunzip -c /var/lib/cwl/stge231293e-9681-4f74-9ef5-ef585ddc06a4/GCF_007992335.1_ASM799233v1_genomic.fna.gz | prodigal -d GCF_007992335.1_ASM799233v1_genomic.fna/cds.fna -a GCF_007992335.1_ASM799233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:08,331] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:08,331] [INFO] Task started: HMMsearch
[2024-01-24 13:49:08,331] [INFO] Running command: hmmsearch --tblout GCF_007992335.1_ASM799233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/reference_markers.hmm GCF_007992335.1_ASM799233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:08,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:08,598] [INFO] Found 6/6 markers.
[2024-01-24 13:49:08,662] [INFO] Query marker FASTA was written to GCF_007992335.1_ASM799233v1_genomic.fna/markers.fasta
[2024-01-24 13:49:08,662] [INFO] Task started: Blastn
[2024-01-24 13:49:08,662] [INFO] Running command: blastn -query GCF_007992335.1_ASM799233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/reference_markers.fasta -out GCF_007992335.1_ASM799233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,237] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:09,238] [INFO] Target genome list was writen to GCF_007992335.1_ASM799233v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:09,279] [INFO] Task started: fastANI
[2024-01-24 13:49:09,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge231293e-9681-4f74-9ef5-ef585ddc06a4/GCF_007992335.1_ASM799233v1_genomic.fna.gz --refList GCF_007992335.1_ASM799233v1_genomic.fna/target_genomes.txt --output GCF_007992335.1_ASM799233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:18,531] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:18,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:18,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:18,549] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:18,549] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:18,549] [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 diolivorans	strain=DSM 14421	GCA_001434255.1	179838	179838	type	True	99.9993	999	1005	95	conclusive
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	79.1202	220	1005	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	79.0263	191	1005	95	below_threshold
Lentilactobacillus buchneri subsp. silagei	strain=SG162	GCA_013167835.1	2737512	1581	type	True	78.9487	222	1005	95	below_threshold
Lentilactobacillus parabuchneri	strain=NBRC 107865	GCA_001591885.1	152331	152331	type	True	78.904	209	1005	95	below_threshold
Lentilactobacillus parabuchneri	strain=DSM 5707	GCA_001435315.1	152331	152331	type	True	78.8941	216	1005	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	78.6414	236	1005	95	below_threshold
Lentilactobacillus kisonensis	strain=DSM 19906	GCA_001434135.1	481722	481722	type	True	78.5725	217	1005	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=DSM 19907	GCA_001436255.1	2944812	481723	type	True	78.4056	218	1005	95	below_threshold
Lentilactobacillus parafarraginis	strain=JCM 14109	GCA_001311355.1	390842	390842	type	True	78.3901	211	1005	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	78.3886	210	1005	95	below_threshold
Lentilactobacillus kisonensis	strain=JCM 15041	GCA_001311425.1	481722	481722	type	True	78.3643	217	1005	95	below_threshold
Lentilactobacillus fungorum	strain=YK48G	GCA_016860605.1	2201250	2201250	type	True	78.0919	211	1005	95	below_threshold
Lentilactobacillus kosonis	strain=NBRC111893	GCA_003864335.1	2810561	2810561	type	True	77.9184	89	1005	95	below_threshold
Lentilactobacillus curieae	strain=CCTCC M 2011381	GCA_000785105.2	1138822	1138822	type	True	77.7218	106	1005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:18,551] [INFO] DFAST Taxonomy check result was written to GCF_007992335.1_ASM799233v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:18,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:18,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:18,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/checkm_data
[2024-01-24 13:49:18,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:18,591] [INFO] Task started: CheckM
[2024-01-24 13:49:18,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992335.1_ASM799233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992335.1_ASM799233v1_genomic.fna/checkm_input GCF_007992335.1_ASM799233v1_genomic.fna/checkm_result
[2024-01-24 13:49:45,780] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:45,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:45,799] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:45,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:45,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992335.1_ASM799233v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:45,800] [INFO] Task started: Blastn
[2024-01-24 13:49:45,800] [INFO] Running command: blastn -query GCF_007992335.1_ASM799233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d1be25a-54f3-4622-a5c7-faab1bd1d227/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992335.1_ASM799233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,598] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:46,598] [INFO] Target genome list was writen to GCF_007992335.1_ASM799233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:46,610] [INFO] Task started: fastANI
[2024-01-24 13:49:46,610] [INFO] Running command: fastANI --query /var/lib/cwl/stge231293e-9681-4f74-9ef5-ef585ddc06a4/GCF_007992335.1_ASM799233v1_genomic.fna.gz --refList GCF_007992335.1_ASM799233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992335.1_ASM799233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:55,468] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,484] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:55,485] [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_001434255.1	s__Lentilactobacillus diolivorans	99.9993	999	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.05	98.10	0.95	0.90	3	conclusive
GCF_007989105.1	s__Lentilactobacillus kefiri	79.1409	219	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	78.8941	216	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_019061365.1	s__Lentilactobacillus sp019061365	78.7086	226	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	78.6414	236	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	78.58	207	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.5725	217	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_001435895.1	s__Lentilactobacillus parafarraginis	78.4066	204	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.53	97.19	0.92	0.88	5	-
GCF_001436255.1	s__Lentilactobacillus rapi	78.4056	218	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	78.1093	210	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900411375.1	s__Lentilactobacillus raoultii	77.902	223	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184075.1	s__Lentilactobacillus kribbianus	77.7879	67	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785105.2	s__Lentilactobacillus curieae	77.7218	106	1005	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,487] [INFO] GTDB search result was written to GCF_007992335.1_ASM799233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:55,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:55,493] [INFO] DFAST_QC result json was written to GCF_007992335.1_ASM799233v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:55,494] [INFO] DFAST_QC completed!
[2024-01-24 13:49:55,494] [INFO] Total running time: 0h0m55s