[2024-01-24 11:26:27,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference
[2024-01-24 11:26:28,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:28,921] [INFO] Task started: Prodigal
[2024-01-24 11:26:28,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgf617fa3f-f553-4926-98a0-a3ef5eb0f967/GCF_018555455.1_ASM1855545v1_genomic.fna.gz | prodigal -d GCF_018555455.1_ASM1855545v1_genomic.fna/cds.fna -a GCF_018555455.1_ASM1855545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,319] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,319] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,319] [INFO] Running command: hmmsearch --tblout GCF_018555455.1_ASM1855545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/reference_markers.hmm GCF_018555455.1_ASM1855545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:38,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:38,620] [INFO] Found 6/6 markers.
[2024-01-24 11:26:38,644] [INFO] Query marker FASTA was written to GCF_018555455.1_ASM1855545v1_genomic.fna/markers.fasta
[2024-01-24 11:26:38,645] [INFO] Task started: Blastn
[2024-01-24 11:26:38,645] [INFO] Running command: blastn -query GCF_018555455.1_ASM1855545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/reference_markers.fasta -out GCF_018555455.1_ASM1855545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:39,586] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:39,589] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:39,589] [INFO] Target genome list was writen to GCF_018555455.1_ASM1855545v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:39,618] [INFO] Task started: fastANI
[2024-01-24 11:26:39,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgf617fa3f-f553-4926-98a0-a3ef5eb0f967/GCF_018555455.1_ASM1855545v1_genomic.fna.gz --refList GCF_018555455.1_ASM1855545v1_genomic.fna/target_genomes.txt --output GCF_018555455.1_ASM1855545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:50,317] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:50,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:50,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:50,328] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:50,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:50,329] [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 colobi	strain=LC6	GCA_018555455.1	2809026	2809026	type	True	100.0	891	891	95	conclusive
Bifidobacterium imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	86.3794	599	891	95	below_threshold
Bifidobacterium saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	86.2778	626	891	95	below_threshold
Bifidobacterium felsineum	strain=TRE H	GCA_002802915.1	2045440	2045440	type	True	86.2624	601	891	95	below_threshold
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	86.2324	617	891	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000771625.1	762210	762210	type	True	86.1729	635	891	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000741715.1	762210	762210	type	True	86.1502	631	891	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.597	563	891	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	82.9168	511	891	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	81.712	383	891	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	79.9907	312	891	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.3661	203	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:50,331] [INFO] DFAST Taxonomy check result was written to GCF_018555455.1_ASM1855545v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:50,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:50,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:50,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/checkm_data
[2024-01-24 11:26:50,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:50,366] [INFO] Task started: CheckM
[2024-01-24 11:26:50,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018555455.1_ASM1855545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018555455.1_ASM1855545v1_genomic.fna/checkm_input GCF_018555455.1_ASM1855545v1_genomic.fna/checkm_result
[2024-01-24 11:27:23,623] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:23,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:23,645] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:23,646] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:23,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018555455.1_ASM1855545v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:23,647] [INFO] Task started: Blastn
[2024-01-24 11:27:23,647] [INFO] Running command: blastn -query GCF_018555455.1_ASM1855545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ec0e2da-0f1d-4fa9-9a50-3504f157cad5/dqc_reference/reference_markers_gtdb.fasta -out GCF_018555455.1_ASM1855545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:24,773] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:24,777] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:24,777] [INFO] Target genome list was writen to GCF_018555455.1_ASM1855545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:24,808] [INFO] Task started: fastANI
[2024-01-24 11:27:24,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgf617fa3f-f553-4926-98a0-a3ef5eb0f967/GCF_018555455.1_ASM1855545v1_genomic.fna.gz --refList GCF_018555455.1_ASM1855545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018555455.1_ASM1855545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:31,652] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:31,662] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:31,662] [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_018555455.1	s__Bifidobacterium sp018555455	100.0	891	891	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_002860405.1	s__Bifidobacterium imperatoris	86.3881	598	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002802915.1	s__Bifidobacterium felsineum	86.2624	601	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_009193305.1	s__Bifidobacterium cebidarum	86.2388	616	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741715.1	s__Bifidobacterium saguini	86.1537	630	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_002802865.1	s__Bifidobacterium scaligerum	84.6447	546	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	84.0349	539	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555355.1	s__Bifidobacterium sp018555355	83.5306	568	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_002259745.1	s__Bifidobacterium myosotis	82.9168	511	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.4539	399	891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	79.9907	312	891	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 11:27:31,669] [INFO] GTDB search result was written to GCF_018555455.1_ASM1855545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:31,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:31,673] [INFO] DFAST_QC result json was written to GCF_018555455.1_ASM1855545v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:31,674] [INFO] DFAST_QC completed!
[2024-01-24 11:27:31,674] [INFO] Total running time: 0h1m4s