[2024-01-24 11:43:42,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference
[2024-01-24 11:43:43,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,782] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg1995edd9-e257-47cc-b7fd-cf3f42cd4dd1/GCF_002706665.1_ASM270666v1_genomic.fna.gz | prodigal -d GCF_002706665.1_ASM270666v1_genomic.fna/cds.fna -a GCF_002706665.1_ASM270666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:51,692] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:51,693] [INFO] Task started: HMMsearch
[2024-01-24 11:43:51,693] [INFO] Running command: hmmsearch --tblout GCF_002706665.1_ASM270666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/reference_markers.hmm GCF_002706665.1_ASM270666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,965] [INFO] Found 6/6 markers.
[2024-01-24 11:43:52,192] [INFO] Query marker FASTA was written to GCF_002706665.1_ASM270666v1_genomic.fna/markers.fasta
[2024-01-24 11:43:52,192] [INFO] Task started: Blastn
[2024-01-24 11:43:52,192] [INFO] Running command: blastn -query GCF_002706665.1_ASM270666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/reference_markers.fasta -out GCF_002706665.1_ASM270666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,158] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,163] [INFO] Selected 9 target genomes.
[2024-01-24 11:43:53,163] [INFO] Target genome list was writen to GCF_002706665.1_ASM270666v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,173] [INFO] Task started: fastANI
[2024-01-24 11:43:53,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg1995edd9-e257-47cc-b7fd-cf3f42cd4dd1/GCF_002706665.1_ASM270666v1_genomic.fna.gz --refList GCF_002706665.1_ASM270666v1_genomic.fna/target_genomes.txt --output GCF_002706665.1_ASM270666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:57,809] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:57,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:57,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:57,818] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:43:57,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:57,818] [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 pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	100.0	657	659	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=LMG 11569	GCA_000741295.1	1690	1694	type	True	99.9659	626	659	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000687595.1	1690	1694	type	True	99.9475	617	659	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	99.9367	606	659	95	conclusive
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	94.1142	560	659	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.6004	326	659	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.7602	310	659	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.9918	93	659	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.7449	118	659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:57,820] [INFO] DFAST Taxonomy check result was written to GCF_002706665.1_ASM270666v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:57,820] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:57,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:57,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/checkm_data
[2024-01-24 11:43:57,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:57,865] [INFO] Task started: CheckM
[2024-01-24 11:43:57,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002706665.1_ASM270666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002706665.1_ASM270666v1_genomic.fna/checkm_input GCF_002706665.1_ASM270666v1_genomic.fna/checkm_result
[2024-01-24 11:44:32,105] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:32,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,122] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:32,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:32,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002706665.1_ASM270666v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:32,123] [INFO] Task started: Blastn
[2024-01-24 11:44:32,123] [INFO] Running command: blastn -query GCF_002706665.1_ASM270666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758e4190-9382-452c-807c-7d28301e33e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002706665.1_ASM270666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:33,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:33,681] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:33,681] [INFO] Target genome list was writen to GCF_002706665.1_ASM270666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:33,709] [INFO] Task started: fastANI
[2024-01-24 11:44:33,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg1995edd9-e257-47cc-b7fd-cf3f42cd4dd1/GCF_002706665.1_ASM270666v1_genomic.fna.gz --refList GCF_002706665.1_ASM270666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002706665.1_ASM270666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:38,411] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:38,420] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:38,420] [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_000741295.1	s__Bifidobacterium globosum	99.9659	626	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	conclusive
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	94.7732	578	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771225.1	s__Bifidobacterium pseudolongum	94.1103	563	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	-
GCF_003952025.1	s__Bifidobacterium castoris	83.0757	474	659	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	82.9634	479	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_002286915.1	s__Bifidobacterium italicum	82.8448	481	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741575.1	s__Bifidobacterium cuniculi	81.5368	389	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	80.66	334	659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	80.2153	323	659	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 11:44:38,422] [INFO] GTDB search result was written to GCF_002706665.1_ASM270666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:38,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:38,425] [INFO] DFAST_QC result json was written to GCF_002706665.1_ASM270666v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:38,425] [INFO] DFAST_QC completed!
[2024-01-24 11:44:38,425] [INFO] Total running time: 0h0m56s