[2024-01-24 13:25:58,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,092] [INFO] DQC Reference Directory: /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg6511b77f-be82-4e5f-b1e9-cb30d5ca36d7/GCF_000771065.1_DSM-17777_genomic.fna.gz | prodigal -d GCF_000771065.1_DSM-17777_genomic.fna/cds.fna -a GCF_000771065.1_DSM-17777_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:07,804] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:07,804] [INFO] Task started: HMMsearch
[2024-01-24 13:26:07,805] [INFO] Running command: hmmsearch --tblout GCF_000771065.1_DSM-17777_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/reference_markers.hmm GCF_000771065.1_DSM-17777_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:08,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:08,051] [INFO] Found 6/6 markers.
[2024-01-24 13:26:08,079] [INFO] Query marker FASTA was written to GCF_000771065.1_DSM-17777_genomic.fna/markers.fasta
[2024-01-24 13:26:08,080] [INFO] Task started: Blastn
[2024-01-24 13:26:08,080] [INFO] Running command: blastn -query GCF_000771065.1_DSM-17777_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/reference_markers.fasta -out GCF_000771065.1_DSM-17777_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:08,946] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:08,955] [INFO] Selected 20 target genomes.
[2024-01-24 13:26:08,956] [INFO] Target genome list was writen to GCF_000771065.1_DSM-17777_genomic.fna/target_genomes.txt
[2024-01-24 13:26:09,003] [INFO] Task started: fastANI
[2024-01-24 13:26:09,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg6511b77f-be82-4e5f-b1e9-cb30d5ca36d7/GCF_000771065.1_DSM-17777_genomic.fna.gz --refList GCF_000771065.1_DSM-17777_genomic.fna/target_genomes.txt --output GCF_000771065.1_DSM-17777_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:17,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:17,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:17,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:17,766] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:17,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:17,769] [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
Bifidobacterium tsurumiense	strain=DSM 17777	GCA_000771065.1	356829	356829	type	True	100.0	699	702	95	conclusive
Bifidobacterium tsurumiense	strain=DSM 17777	GCA_000429745.1	356829	356829	type	True	99.999	701	702	95	conclusive
Bifidobacterium tsurumiense	strain=JCM 13495	GCA_000741765.1	356829	356829	type	True	99.9879	696	702	95	conclusive
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	78.5672	123	702	95	below_threshold
Bifidobacterium moukalabense	strain=GG01	GCA_005405645.1	1333651	1333651	type	True	78.5084	127	702	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	78.2724	108	702	95	below_threshold
Bifidobacterium boum	strain=LMG 10736	GCA_000741535.1	78343	78343	type	True	78.2424	109	702	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	78.2242	126	702	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	78.1553	129	702	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	78.129	114	702	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	78.0897	115	702	95	below_threshold
Bifidobacterium saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	77.7446	145	702	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000741715.1	762210	762210	type	True	77.7164	143	702	95	below_threshold
Bifidobacterium crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	77.7063	83	702	95	below_threshold
Bifidobacterium tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	77.4458	112	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:17,772] [INFO] DFAST Taxonomy check result was written to GCF_000771065.1_DSM-17777_genomic.fna/tc_result.tsv
[2024-01-24 13:26:17,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:17,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:17,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/checkm_data
[2024-01-24 13:26:17,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:17,804] [INFO] Task started: CheckM
[2024-01-24 13:26:17,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771065.1_DSM-17777_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771065.1_DSM-17777_genomic.fna/checkm_input GCF_000771065.1_DSM-17777_genomic.fna/checkm_result
[2024-01-24 13:26:46,549] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:46,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:46,574] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:46,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:46,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771065.1_DSM-17777_genomic.fna/markers.fasta)
[2024-01-24 13:26:46,575] [INFO] Task started: Blastn
[2024-01-24 13:26:46,575] [INFO] Running command: blastn -query GCF_000771065.1_DSM-17777_genomic.fna/markers.fasta -db /var/lib/cwl/stg65ddab05-7da7-4c8d-a32f-ca269f108712/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771065.1_DSM-17777_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:47,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:47,621] [INFO] Selected 21 target genomes.
[2024-01-24 13:26:47,622] [INFO] Target genome list was writen to GCF_000771065.1_DSM-17777_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:47,637] [INFO] Task started: fastANI
[2024-01-24 13:26:47,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg6511b77f-be82-4e5f-b1e9-cb30d5ca36d7/GCF_000771065.1_DSM-17777_genomic.fna.gz --refList GCF_000771065.1_DSM-17777_genomic.fna/target_genomes_gtdb.txt --output GCF_000771065.1_DSM-17777_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:56,281] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:56,304] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:56,304] [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_000741765.1	s__Bifidobacterium tsurumiense	99.9879	696	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.58	0.98	0.96	4	conclusive
GCF_000522505.1	s__Bifidobacterium moukalabense	78.5672	123	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_002802875.1	s__Galliscardovia primatium	78.408	81	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741535.1	s__Bifidobacterium boum	78.2424	109	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	-
GCF_012932375.1	s__Bifidobacterium sp012932375	78.1958	114	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	78.1553	129	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_002742445.1	s__Bifidobacterium sp002742445	78.0996	132	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_900129045.1	s__Bifidobacterium merycicum	78.0795	119	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_000010425.1	s__Bifidobacterium adolescentis	78.0744	125	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_001025195.1	s__Bifidobacterium catenulatum	78.0483	132	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_014898155.1	s__Bifidobacterium eulemuris	78.0417	118	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	78.0253	136	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_014898175.1	s__Bifidobacterium lemurum	78.0205	115	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002802915.1	s__Bifidobacterium felsineum	77.9719	127	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_002860405.1	s__Bifidobacterium imperatoris	77.8509	124	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012932425.1	s__Bifidobacterium sp012932425	77.8273	126	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	77.7473	95	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741715.1	s__Bifidobacterium saguini	77.7164	143	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_000738005.1	s__Bifidobacterium crudilactis	77.7063	83	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	77.4458	112	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	77.0571	73	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:56,306] [INFO] GTDB search result was written to GCF_000771065.1_DSM-17777_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:56,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:56,314] [INFO] DFAST_QC result json was written to GCF_000771065.1_DSM-17777_genomic.fna/dqc_result.json
[2024-01-24 13:26:56,314] [INFO] DFAST_QC completed!
[2024-01-24 13:26:56,314] [INFO] Total running time: 0h0m58s