[2024-01-24 12:54:22,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,521] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference
[2024-01-24 12:54:24,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:24,063] [INFO] Task started: Prodigal
[2024-01-24 12:54:24,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf7a6b7b-1478-45bf-872c-ebe6007a6b46/GCF_900411375.1_PRJEB20856_genomic.fna.gz | prodigal -d GCF_900411375.1_PRJEB20856_genomic.fna/cds.fna -a GCF_900411375.1_PRJEB20856_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:30,985] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:30,986] [INFO] Task started: HMMsearch
[2024-01-24 12:54:30,986] [INFO] Running command: hmmsearch --tblout GCF_900411375.1_PRJEB20856_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/reference_markers.hmm GCF_900411375.1_PRJEB20856_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:31,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:31,256] [INFO] Found 6/6 markers.
[2024-01-24 12:54:31,288] [INFO] Query marker FASTA was written to GCF_900411375.1_PRJEB20856_genomic.fna/markers.fasta
[2024-01-24 12:54:31,288] [INFO] Task started: Blastn
[2024-01-24 12:54:31,288] [INFO] Running command: blastn -query GCF_900411375.1_PRJEB20856_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/reference_markers.fasta -out GCF_900411375.1_PRJEB20856_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:31,880] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:31,887] [INFO] Selected 19 target genomes.
[2024-01-24 12:54:31,888] [INFO] Target genome list was writen to GCF_900411375.1_PRJEB20856_genomic.fna/target_genomes.txt
[2024-01-24 12:54:31,925] [INFO] Task started: fastANI
[2024-01-24 12:54:31,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7a6b7b-1478-45bf-872c-ebe6007a6b46/GCF_900411375.1_PRJEB20856_genomic.fna.gz --refList GCF_900411375.1_PRJEB20856_genomic.fna/target_genomes.txt --output GCF_900411375.1_PRJEB20856_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:40,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:40,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:40,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:40,295] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:40,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:40,295] [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 raoultii	strain=Marseille-P4006	GCA_900411375.1	1987503	1987503	type	True	100.0	1010	1011	95	conclusive
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_004354795.1	1588	1588	type	True	79.8593	396	1011	95	below_threshold
Lentilactobacillus hilgardii	strain=DSM 20176	GCA_001434655.1	1588	1588	type	True	79.7287	392	1011	95	below_threshold
Lentilactobacillus farraginis	strain=DSM 18382	GCA_001435875.1	390841	390841	type	True	79.725	424	1011	95	below_threshold
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_000159315.1	1588	1588	type	True	79.6826	410	1011	95	below_threshold
Lentilactobacillus farraginis	strain=JCM 14108	GCA_000583655.1	390841	390841	type	True	79.6627	424	1011	95	below_threshold
Lentilactobacillus parafarraginis	strain=DSM 18390	GCA_001435895.1	390842	390842	type	True	78.9002	272	1011	95	below_threshold
Lentilactobacillus parafarraginis	strain=JCM 14109	GCA_001311355.1	390842	390842	type	True	78.7986	266	1011	95	below_threshold
Lentilactobacillus fungorum	strain=YK48G	GCA_016860605.1	2201250	2201250	type	True	78.1212	184	1011	95	below_threshold
Lentilactobacillus kisonensis	strain=DSM 19906	GCA_001434135.1	481722	481722	type	True	78.1045	184	1011	95	below_threshold
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	77.9384	167	1011	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=DSM 19907	GCA_001436255.1	2944812	481723	type	True	77.9382	177	1011	95	below_threshold
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	77.9121	192	1011	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	77.8638	186	1011	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	77.8614	171	1011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:40,297] [INFO] DFAST Taxonomy check result was written to GCF_900411375.1_PRJEB20856_genomic.fna/tc_result.tsv
[2024-01-24 12:54:40,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:40,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:40,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/checkm_data
[2024-01-24 12:54:40,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:40,337] [INFO] Task started: CheckM
[2024-01-24 12:54:40,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900411375.1_PRJEB20856_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900411375.1_PRJEB20856_genomic.fna/checkm_input GCF_900411375.1_PRJEB20856_genomic.fna/checkm_result
[2024-01-24 12:55:07,743] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:07,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:07,769] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:07,769] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:07,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900411375.1_PRJEB20856_genomic.fna/markers.fasta)
[2024-01-24 12:55:07,770] [INFO] Task started: Blastn
[2024-01-24 12:55:07,770] [INFO] Running command: blastn -query GCF_900411375.1_PRJEB20856_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ed0c72-8b11-45bf-a9e3-87e7de17d02d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900411375.1_PRJEB20856_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:08,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:08,545] [INFO] Selected 18 target genomes.
[2024-01-24 12:55:08,545] [INFO] Target genome list was writen to GCF_900411375.1_PRJEB20856_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:08,565] [INFO] Task started: fastANI
[2024-01-24 12:55:08,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7a6b7b-1478-45bf-872c-ebe6007a6b46/GCF_900411375.1_PRJEB20856_genomic.fna.gz --refList GCF_900411375.1_PRJEB20856_genomic.fna/target_genomes_gtdb.txt --output GCF_900411375.1_PRJEB20856_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:16,419] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:16,433] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:16,434] [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_900411375.1	s__Lentilactobacillus raoultii	100.0	1010	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000159315.1	s__Lentilactobacillus hilgardii	79.697	408	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.37	96.88	0.92	0.87	10	-
GCF_000583655.1	s__Lentilactobacillus farraginis	79.6627	424	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001435895.1	s__Lentilactobacillus parafarraginis	78.9002	272	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.53	97.19	0.92	0.88	5	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	78.1795	176	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.1243	183	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	78.1212	184	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434255.1	s__Lentilactobacillus diolivorans	77.9906	243	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.05	98.10	0.95	0.90	3	-
GCF_001436255.1	s__Lentilactobacillus rapi	77.9382	177	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_019061365.1	s__Lentilactobacillus sp019061365	77.9359	170	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	-
GCF_007989105.1	s__Lentilactobacillus kefiri	77.9121	192	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	77.8638	186	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCA_002418005.1	s__Lentilactobacillus sp002418005	77.0041	91	1011	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.90	99.90	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:16,435] [INFO] GTDB search result was written to GCF_900411375.1_PRJEB20856_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:16,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:16,439] [INFO] DFAST_QC result json was written to GCF_900411375.1_PRJEB20856_genomic.fna/dqc_result.json
[2024-01-24 12:55:16,439] [INFO] DFAST_QC completed!
[2024-01-24 12:55:16,440] [INFO] Total running time: 0h0m54s