[2024-01-24 14:19:02,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference
[2024-01-24 14:19:04,192] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:04,193] [INFO] Task started: Prodigal
[2024-01-24 14:19:04,194] [INFO] Running command: gunzip -c /var/lib/cwl/stga9f108ec-74a8-4172-b9cd-c32d12875166/GCF_000426425.1_ASM42642v1_genomic.fna.gz | prodigal -d GCF_000426425.1_ASM42642v1_genomic.fna/cds.fna -a GCF_000426425.1_ASM42642v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:12,351] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:12,352] [INFO] Task started: HMMsearch
[2024-01-24 14:19:12,352] [INFO] Running command: hmmsearch --tblout GCF_000426425.1_ASM42642v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/reference_markers.hmm GCF_000426425.1_ASM42642v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:12,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:12,597] [INFO] Found 6/6 markers.
[2024-01-24 14:19:12,618] [INFO] Query marker FASTA was written to GCF_000426425.1_ASM42642v1_genomic.fna/markers.fasta
[2024-01-24 14:19:12,618] [INFO] Task started: Blastn
[2024-01-24 14:19:12,618] [INFO] Running command: blastn -query GCF_000426425.1_ASM42642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/reference_markers.fasta -out GCF_000426425.1_ASM42642v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:13,569] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:13,572] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:13,572] [INFO] Target genome list was writen to GCF_000426425.1_ASM42642v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:13,599] [INFO] Task started: fastANI
[2024-01-24 14:19:13,599] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f108ec-74a8-4172-b9cd-c32d12875166/GCF_000426425.1_ASM42642v1_genomic.fna.gz --refList GCF_000426425.1_ASM42642v1_genomic.fna/target_genomes.txt --output GCF_000426425.1_ASM42642v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:19,237] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:19,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:19,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:19,249] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:19:19,250] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:19:19,250] [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 thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	100.0	729	732	95	inconclusive
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000771005.1	79262	246618	type	True	99.9963	711	732	95	inconclusive
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	99.9859	730	732	95	inconclusive
Bifidobacterium porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	95.7194	612	732	95	inconclusive
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	86.4205	594	732	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	85.802	521	732	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.6425	288	732	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.5668	269	732	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.658	213	732	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	77.2462	78	732	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	75.6956	60	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:19,251] [INFO] DFAST Taxonomy check result was written to GCF_000426425.1_ASM42642v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:19,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:19,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:19,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/checkm_data
[2024-01-24 14:19:19,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:19,278] [INFO] Task started: CheckM
[2024-01-24 14:19:19,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426425.1_ASM42642v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426425.1_ASM42642v1_genomic.fna/checkm_input GCF_000426425.1_ASM42642v1_genomic.fna/checkm_result
[2024-01-24 14:19:48,220] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:48,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:48,240] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:48,240] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:48,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426425.1_ASM42642v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:48,241] [INFO] Task started: Blastn
[2024-01-24 14:19:48,242] [INFO] Running command: blastn -query GCF_000426425.1_ASM42642v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b76907-3054-446c-b9a7-ea7a777e41df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426425.1_ASM42642v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:49,832] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:49,835] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:49,835] [INFO] Target genome list was writen to GCF_000426425.1_ASM42642v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:49,866] [INFO] Task started: fastANI
[2024-01-24 14:19:49,866] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f108ec-74a8-4172-b9cd-c32d12875166/GCF_000426425.1_ASM42642v1_genomic.fna.gz --refList GCF_000426425.1_ASM42642v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426425.1_ASM42642v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:19:57,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,621] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:19:57,621] [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
GCA_000771265.1	s__Bifidobacterium thermophilum	95.6061	626	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	conclusive
GCA_000741495.1	s__Bifidobacterium thermophilum_A	87.8435	519	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299485.1	s__Bifidobacterium apri	86.4205	594	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741535.1	s__Bifidobacterium boum	85.6994	534	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.8971	284	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	79.7573	270	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451435.1	s__Bifidobacterium sp002451435	79.6663	237	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.6598	295	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.6318	247	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003952945.1	s__Bifidobacterium samirii	79.5447	267	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	79.3998	251	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_002259745.1	s__Bifidobacterium myosotis	79.3897	266	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_000522505.1	s__Bifidobacterium moukalabense	79.1794	262	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,623] [INFO] GTDB search result was written to GCF_000426425.1_ASM42642v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:19:57,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:19:57,627] [INFO] DFAST_QC result json was written to GCF_000426425.1_ASM42642v1_genomic.fna/dqc_result.json
[2024-01-24 14:19:57,627] [INFO] DFAST_QC completed!
[2024-01-24 14:19:57,628] [INFO] Total running time: 0h0m55s