[2024-01-24 11:44:23,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference
[2024-01-24 11:44:26,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,344] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg493f8287-a4ed-4f3b-b0ad-121eea1ef363/GCF_003952025.1_ASM395202v1_genomic.fna.gz | prodigal -d GCF_003952025.1_ASM395202v1_genomic.fna/cds.fna -a GCF_003952025.1_ASM395202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,130] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,130] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,130] [INFO] Running command: hmmsearch --tblout GCF_003952025.1_ASM395202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/reference_markers.hmm GCF_003952025.1_ASM395202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,379] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,381] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,406] [INFO] Query marker FASTA was written to GCF_003952025.1_ASM395202v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,407] [INFO] Task started: Blastn
[2024-01-24 11:44:34,407] [INFO] Running command: blastn -query GCF_003952025.1_ASM395202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/reference_markers.fasta -out GCF_003952025.1_ASM395202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,525] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,529] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:35,529] [INFO] Target genome list was writen to GCF_003952025.1_ASM395202v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,534] [INFO] Task started: fastANI
[2024-01-24 11:44:35,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg493f8287-a4ed-4f3b-b0ad-121eea1ef363/GCF_003952025.1_ASM395202v1_genomic.fna.gz --refList GCF_003952025.1_ASM395202v1_genomic.fna/target_genomes.txt --output GCF_003952025.1_ASM395202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:41,154] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:41,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:41,165] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:41,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:41,166] [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 castoris	strain=2020B	GCA_003952025.1	2306972	2306972	type	True	100.0	818	821	95	conclusive
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	93.7604	608	821	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	92.0554	597	821	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000771425.1	35760	35760	type	True	92.0493	556	821	95	below_threshold
Bifidobacterium choerinum	strain=LMG 10510	GCA_000741135.1	35760	35760	type	True	91.91	608	821	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	82.7262	479	821	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.3411	379	821	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.6759	350	821	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.7502	189	821	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.492	144	821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,168] [INFO] DFAST Taxonomy check result was written to GCF_003952025.1_ASM395202v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:41,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:41,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:41,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/checkm_data
[2024-01-24 11:44:41,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:41,197] [INFO] Task started: CheckM
[2024-01-24 11:44:41,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003952025.1_ASM395202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003952025.1_ASM395202v1_genomic.fna/checkm_input GCF_003952025.1_ASM395202v1_genomic.fna/checkm_result
[2024-01-24 11:45:09,296] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:09,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:09,318] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:09,319] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:09,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003952025.1_ASM395202v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:09,319] [INFO] Task started: Blastn
[2024-01-24 11:45:09,320] [INFO] Running command: blastn -query GCF_003952025.1_ASM395202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0babd1bc-6b44-4bf5-9f59-8551ed88721f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003952025.1_ASM395202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:11,243] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:11,246] [INFO] Selected 5 target genomes.
[2024-01-24 11:45:11,247] [INFO] Target genome list was writen to GCF_003952025.1_ASM395202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:11,250] [INFO] Task started: fastANI
[2024-01-24 11:45:11,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg493f8287-a4ed-4f3b-b0ad-121eea1ef363/GCF_003952025.1_ASM395202v1_genomic.fna.gz --refList GCF_003952025.1_ASM395202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003952025.1_ASM395202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:14,226] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:14,232] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:14,232] [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_003952025.1	s__Bifidobacterium castoris	100.0	818	821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002286915.1	s__Bifidobacterium italicum	93.7604	608	821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741135.1	s__Bifidobacterium choerinum	91.91	608	821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_002860345.1	s__Bifidobacterium anseris	91.4912	624	821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.21	99.21	0.95	0.95	2	-
GCF_002286935.1	s__Bifidobacterium criceti	86.6497	551	821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.26	97.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:14,234] [INFO] GTDB search result was written to GCF_003952025.1_ASM395202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:14,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:14,238] [INFO] DFAST_QC result json was written to GCF_003952025.1_ASM395202v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:14,238] [INFO] DFAST_QC completed!
[2024-01-24 11:45:14,239] [INFO] Total running time: 0h0m51s