[2024-01-24 11:20:04,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference
[2024-01-24 11:20:05,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,355] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg649fc27b-9742-47f7-b280-30109c753eb8/GCF_002259715.1_ASM225971v1_genomic.fna.gz | prodigal -d GCF_002259715.1_ASM225971v1_genomic.fna/cds.fna -a GCF_002259715.1_ASM225971v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:13,406] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:13,407] [INFO] Task started: HMMsearch
[2024-01-24 11:20:13,407] [INFO] Running command: hmmsearch --tblout GCF_002259715.1_ASM225971v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/reference_markers.hmm GCF_002259715.1_ASM225971v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:13,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:13,598] [INFO] Found 6/6 markers.
[2024-01-24 11:20:13,617] [INFO] Query marker FASTA was written to GCF_002259715.1_ASM225971v1_genomic.fna/markers.fasta
[2024-01-24 11:20:13,618] [INFO] Task started: Blastn
[2024-01-24 11:20:13,618] [INFO] Running command: blastn -query GCF_002259715.1_ASM225971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/reference_markers.fasta -out GCF_002259715.1_ASM225971v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:14,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:14,455] [INFO] Selected 21 target genomes.
[2024-01-24 11:20:14,455] [INFO] Target genome list was writen to GCF_002259715.1_ASM225971v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:14,476] [INFO] Task started: fastANI
[2024-01-24 11:20:14,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg649fc27b-9742-47f7-b280-30109c753eb8/GCF_002259715.1_ASM225971v1_genomic.fna.gz --refList GCF_002259715.1_ASM225971v1_genomic.fna/target_genomes.txt --output GCF_002259715.1_ASM225971v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:24,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:24,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:24,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:24,082] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:24,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:24,082] [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
Pseudoscardovia suis	strain=DSM 24744	GCA_002259715.1	987063	987063	type	True	100.0	744	745	95	conclusive
Pseudoscardovia suis	strain=DSM 24744	GCA_002797875.1	987063	987063	type	True	99.9884	731	745	95	conclusive
Pseudoscardovia radai	strain=DSM 24742	GCA_002259605.1	987066	987066	type	True	82.2902	417	745	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	79.3182	197	745	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	79.2446	208	745	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	79.1988	190	745	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	79.1723	181	745	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	79.0948	215	745	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.0607	207	745	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	79.0498	204	745	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.014	201	745	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	78.901	193	745	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	78.7798	197	745	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	78.7765	191	745	95	below_threshold
Bifidobacterium colobi	strain=LC6	GCA_018555455.1	2809026	2809026	type	True	78.5961	150	745	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	78.4968	203	745	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.1267	159	745	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	77.3744	68	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:24,084] [INFO] DFAST Taxonomy check result was written to GCF_002259715.1_ASM225971v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:24,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:24,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:24,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/checkm_data
[2024-01-24 11:20:24,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:24,109] [INFO] Task started: CheckM
[2024-01-24 11:20:24,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259715.1_ASM225971v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259715.1_ASM225971v1_genomic.fna/checkm_input GCF_002259715.1_ASM225971v1_genomic.fna/checkm_result
[2024-01-24 11:20:53,111] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:53,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:53,127] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:53,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:53,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259715.1_ASM225971v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:53,128] [INFO] Task started: Blastn
[2024-01-24 11:20:53,128] [INFO] Running command: blastn -query GCF_002259715.1_ASM225971v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3b25088-2895-430d-810c-bfb39716e24c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259715.1_ASM225971v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:54,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:54,303] [INFO] Selected 18 target genomes.
[2024-01-24 11:20:54,303] [INFO] Target genome list was writen to GCF_002259715.1_ASM225971v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:54,333] [INFO] Task started: fastANI
[2024-01-24 11:20:54,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg649fc27b-9742-47f7-b280-30109c753eb8/GCF_002259715.1_ASM225971v1_genomic.fna.gz --refList GCF_002259715.1_ASM225971v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259715.1_ASM225971v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:03,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:03,290] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:03,290] [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_002797875.1	s__Pseudoscardovia suis	99.9884	731	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia	95.0	96.86	96.17	0.92	0.88	7	conclusive
GCF_002259605.1	s__Pseudoscardovia radai	82.3393	416	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353815.1	s__Pseudoscardovia sp002353815	81.5498	336	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234915.1	s__Galliscardovia vansinderenii	79.4465	187	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	79.3431	196	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	79.2332	209	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932365.1	s__Bifidobacterium sp012932365	79.1656	218	745	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	79.1487	182	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.1184	209	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	79.1052	214	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	79.0929	195	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003129925.1	s__Galliscardovia catulorum	78.9692	184	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	78.8006	196	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	78.7642	192	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_018555455.1	s__Bifidobacterium sp018555455	78.5961	150	745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932445.1	s__Bifidobacterium sp012932445	78.4467	107	745	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 11:21:03,292] [INFO] GTDB search result was written to GCF_002259715.1_ASM225971v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:03,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:03,296] [INFO] DFAST_QC result json was written to GCF_002259715.1_ASM225971v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:03,296] [INFO] DFAST_QC completed!
[2024-01-24 11:21:03,296] [INFO] Total running time: 0h0m59s