[2024-01-24 13:08:58,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,462] [INFO] DQC Reference Directory: /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference
[2024-01-24 13:08:59,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,708] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7f13b73-1d4c-4c0f-a87e-d1bd30b918cb/GCF_000421685.1_ASM42168v1_genomic.fna.gz | prodigal -d GCF_000421685.1_ASM42168v1_genomic.fna/cds.fna -a GCF_000421685.1_ASM42168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:05,514] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:05,514] [INFO] Task started: HMMsearch
[2024-01-24 13:09:05,515] [INFO] Running command: hmmsearch --tblout GCF_000421685.1_ASM42168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/reference_markers.hmm GCF_000421685.1_ASM42168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:05,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:05,729] [INFO] Found 6/6 markers.
[2024-01-24 13:09:05,748] [INFO] Query marker FASTA was written to GCF_000421685.1_ASM42168v1_genomic.fna/markers.fasta
[2024-01-24 13:09:05,748] [INFO] Task started: Blastn
[2024-01-24 13:09:05,748] [INFO] Running command: blastn -query GCF_000421685.1_ASM42168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/reference_markers.fasta -out GCF_000421685.1_ASM42168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:06,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:06,517] [INFO] Selected 20 target genomes.
[2024-01-24 13:09:06,517] [INFO] Target genome list was writen to GCF_000421685.1_ASM42168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:06,548] [INFO] Task started: fastANI
[2024-01-24 13:09:06,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f13b73-1d4c-4c0f-a87e-d1bd30b918cb/GCF_000421685.1_ASM42168v1_genomic.fna.gz --refList GCF_000421685.1_ASM42168v1_genomic.fna/target_genomes.txt --output GCF_000421685.1_ASM42168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:17,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:17,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:17,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:17,145] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:09:17,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:17,146] [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 minimum	strain=DSM 20102	GCA_000421685.1	1693	1693	type	True	100.0	608	608	95	conclusive
Bifidobacterium minimum	strain=LMG 11592	GCA_000741645.1	1693	1693	type	True	99.9886	607	608	95	conclusive
Bifidobacterium minimum	strain=DSM 20102	GCA_000771245.1	1693	1693	type	True	99.9574	589	608	95	conclusive
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	78.9252	204	608	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	78.8883	212	608	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	78.8092	186	608	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	78.5736	206	608	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	78.5377	196	608	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	78.5366	212	608	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	78.3913	190	608	95	below_threshold
Bifidobacterium vespertilionis	strain=RST16	GCA_008698145.1	2562524	2562524	type	True	78.3695	192	608	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	78.3655	199	608	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	78.2806	208	608	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	78.2314	56	608	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	78.1671	182	608	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.9178	215	608	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	75.8809	54	608	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.1799	57	608	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	75.1581	54	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:17,147] [INFO] DFAST Taxonomy check result was written to GCF_000421685.1_ASM42168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:17,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:17,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:17,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/checkm_data
[2024-01-24 13:09:17,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:17,169] [INFO] Task started: CheckM
[2024-01-24 13:09:17,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421685.1_ASM42168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421685.1_ASM42168v1_genomic.fna/checkm_input GCF_000421685.1_ASM42168v1_genomic.fna/checkm_result
[2024-01-24 13:09:39,947] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:39,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:39,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:39,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:39,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421685.1_ASM42168v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:39,971] [INFO] Task started: Blastn
[2024-01-24 13:09:39,971] [INFO] Running command: blastn -query GCF_000421685.1_ASM42168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7780792-a33a-4898-8f3c-0ae22592fd65/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421685.1_ASM42168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:41,045] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:41,050] [INFO] Selected 25 target genomes.
[2024-01-24 13:09:41,051] [INFO] Target genome list was writen to GCF_000421685.1_ASM42168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:41,408] [INFO] Task started: fastANI
[2024-01-24 13:09:41,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f13b73-1d4c-4c0f-a87e-d1bd30b918cb/GCF_000421685.1_ASM42168v1_genomic.fna.gz --refList GCF_000421685.1_ASM42168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421685.1_ASM42168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:09:53,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:53,681] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:09:53,682] [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_000741645.1	s__Bifidobacterium minimum	99.9886	607	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_000741285.1	s__Bifidobacterium mongoliense	78.9497	208	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_000741775.1	s__Bifidobacterium subtile	78.9175	210	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	78.8092	186	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	78.7288	195	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_000771405.1	s__Bifidobacterium pullorum	78.577	203	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_001042635.1	s__Bifidobacterium scardovii	78.5441	230	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_009299475.1	s__Bifidobacterium avesanii	78.5175	197	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012932365.1	s__Bifidobacterium sp012932365	78.5168	211	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898175.1	s__Bifidobacterium lemurum	78.4883	196	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	78.4813	174	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	78.4228	201	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001025135.1	s__Bifidobacterium bifidum	78.4181	180	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	-
GCA_002451435.1	s__Bifidobacterium sp002451435	78.3862	164	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000741135.1	s__Bifidobacterium choerinum	78.3456	190	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_008698145.1	s__Bifidobacterium vespertilionis	78.3301	194	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	78.3047	209	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	78.2985	207	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	78.2182	179	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667615.1	s__Bifidobacterium choloepi	78.185	183	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	78.1806	182	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_003315635.1	s__Bifidobacterium aemilianum	77.8736	135	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	75.1581	54	608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:09:53,684] [INFO] GTDB search result was written to GCF_000421685.1_ASM42168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:09:53,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:09:53,688] [INFO] DFAST_QC result json was written to GCF_000421685.1_ASM42168v1_genomic.fna/dqc_result.json
[2024-01-24 13:09:53,689] [INFO] DFAST_QC completed!
[2024-01-24 13:09:53,689] [INFO] Total running time: 0h0m55s