[2024-01-24 12:34:20,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference
[2024-01-24 12:34:21,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,766] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb70ddaa-3a11-4331-bfe1-e4ce56385ae1/GCF_002860405.1_ASM286040v1_genomic.fna.gz | prodigal -d GCF_002860405.1_ASM286040v1_genomic.fna/cds.fna -a GCF_002860405.1_ASM286040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:30,462] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:30,463] [INFO] Task started: HMMsearch
[2024-01-24 12:34:30,463] [INFO] Running command: hmmsearch --tblout GCF_002860405.1_ASM286040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/reference_markers.hmm GCF_002860405.1_ASM286040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:30,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:30,709] [INFO] Found 6/6 markers.
[2024-01-24 12:34:30,737] [INFO] Query marker FASTA was written to GCF_002860405.1_ASM286040v1_genomic.fna/markers.fasta
[2024-01-24 12:34:30,737] [INFO] Task started: Blastn
[2024-01-24 12:34:30,737] [INFO] Running command: blastn -query GCF_002860405.1_ASM286040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/reference_markers.fasta -out GCF_002860405.1_ASM286040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:31,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:31,507] [INFO] Selected 12 target genomes.
[2024-01-24 12:34:31,508] [INFO] Target genome list was writen to GCF_002860405.1_ASM286040v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:31,514] [INFO] Task started: fastANI
[2024-01-24 12:34:31,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb70ddaa-3a11-4331-bfe1-e4ce56385ae1/GCF_002860405.1_ASM286040v1_genomic.fna.gz --refList GCF_002860405.1_ASM286040v1_genomic.fna/target_genomes.txt --output GCF_002860405.1_ASM286040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:39,026] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:39,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:39,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:39,038] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:39,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:39,038] [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 imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	100.0	843	848	95	conclusive
Bifidobacterium saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	94.0699	716	848	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000771625.1	762210	762210	type	True	94.0333	714	848	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000741715.1	762210	762210	type	True	93.9398	720	848	95	below_threshold
Bifidobacterium felsineum	strain=TRE H	GCA_002802915.1	2045440	2045440	type	True	86.5629	605	848	95	below_threshold
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	85.9795	575	848	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.804	483	848	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	79.8082	279	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:39,040] [INFO] DFAST Taxonomy check result was written to GCF_002860405.1_ASM286040v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:39,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:39,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:39,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/checkm_data
[2024-01-24 12:34:39,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:39,068] [INFO] Task started: CheckM
[2024-01-24 12:34:39,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002860405.1_ASM286040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002860405.1_ASM286040v1_genomic.fna/checkm_input GCF_002860405.1_ASM286040v1_genomic.fna/checkm_result
[2024-01-24 12:35:09,247] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:09,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:09,267] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:09,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:09,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002860405.1_ASM286040v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:09,268] [INFO] Task started: Blastn
[2024-01-24 12:35:09,268] [INFO] Running command: blastn -query GCF_002860405.1_ASM286040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg868508b8-395e-4dd7-a089-010f5525c9e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002860405.1_ASM286040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:10,360] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:10,364] [INFO] Selected 10 target genomes.
[2024-01-24 12:35:10,364] [INFO] Target genome list was writen to GCF_002860405.1_ASM286040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:10,371] [INFO] Task started: fastANI
[2024-01-24 12:35:10,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb70ddaa-3a11-4331-bfe1-e4ce56385ae1/GCF_002860405.1_ASM286040v1_genomic.fna.gz --refList GCF_002860405.1_ASM286040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002860405.1_ASM286040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:16,358] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:16,370] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:16,370] [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_002860405.1	s__Bifidobacterium imperatoris	100.0	843	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000741715.1	s__Bifidobacterium saguini	93.9398	720	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_002802915.1	s__Bifidobacterium felsineum	86.5525	606	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_018555455.1	s__Bifidobacterium sp018555455	86.3724	592	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193305.1	s__Bifidobacterium cebidarum	85.9795	575	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802865.1	s__Bifidobacterium scaligerum	83.569	492	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741695.1	s__Bifidobacterium reuteri	82.6277	494	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_000196555.1	s__Bifidobacterium longum	82.5129	425	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_001042595.1	s__Bifidobacterium dentium	79.7861	281	848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_003951975.1	s__Bifidobacterium dolichotidis	77.9609	100	848	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 12:35:16,372] [INFO] GTDB search result was written to GCF_002860405.1_ASM286040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:16,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:16,376] [INFO] DFAST_QC result json was written to GCF_002860405.1_ASM286040v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:16,376] [INFO] DFAST_QC completed!
[2024-01-24 12:35:16,376] [INFO] Total running time: 0h0m56s