[2024-01-24 13:32:35,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference
[2024-01-24 13:32:36,407] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,408] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg34de8df6-fa09-4a9f-822a-3ee47ad868d4/GCF_000771565.1_DSM-22366_genomic.fna.gz | prodigal -d GCF_000771565.1_DSM-22366_genomic.fna/cds.fna -a GCF_000771565.1_DSM-22366_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,530] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,530] [INFO] Running command: hmmsearch --tblout GCF_000771565.1_DSM-22366_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/reference_markers.hmm GCF_000771565.1_DSM-22366_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:45,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:45,855] [INFO] Found 6/6 markers.
[2024-01-24 13:32:45,886] [INFO] Query marker FASTA was written to GCF_000771565.1_DSM-22366_genomic.fna/markers.fasta
[2024-01-24 13:32:45,886] [INFO] Task started: Blastn
[2024-01-24 13:32:45,886] [INFO] Running command: blastn -query GCF_000771565.1_DSM-22366_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/reference_markers.fasta -out GCF_000771565.1_DSM-22366_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:46,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:46,629] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:46,629] [INFO] Target genome list was writen to GCF_000771565.1_DSM-22366_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,635] [INFO] Task started: fastANI
[2024-01-24 13:32:46,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg34de8df6-fa09-4a9f-822a-3ee47ad868d4/GCF_000771565.1_DSM-22366_genomic.fna.gz --refList GCF_000771565.1_DSM-22366_genomic.fna/target_genomes.txt --output GCF_000771565.1_DSM-22366_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,795] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:55,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,795] [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 psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	100.0	844	845	95	conclusive
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	99.9986	842	845	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	99.9948	843	845	95	conclusive
Bifidobacterium crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	80.8083	388	845	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	77.701	135	845	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	77.6331	160	845	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	77.6139	156	845	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	77.5931	162	845	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	77.4351	138	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,798] [INFO] DFAST Taxonomy check result was written to GCF_000771565.1_DSM-22366_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/checkm_data
[2024-01-24 13:32:55,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,838] [INFO] Task started: CheckM
[2024-01-24 13:32:55,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771565.1_DSM-22366_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771565.1_DSM-22366_genomic.fna/checkm_input GCF_000771565.1_DSM-22366_genomic.fna/checkm_result
[2024-01-24 13:33:28,608] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:28,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:28,628] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:28,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:28,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771565.1_DSM-22366_genomic.fna/markers.fasta)
[2024-01-24 13:33:28,629] [INFO] Task started: Blastn
[2024-01-24 13:33:28,629] [INFO] Running command: blastn -query GCF_000771565.1_DSM-22366_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25b2ee2-4209-4d71-9dc3-f5e47f28c9d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771565.1_DSM-22366_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:29,564] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:29,568] [INFO] Selected 23 target genomes.
[2024-01-24 13:33:29,568] [INFO] Target genome list was writen to GCF_000771565.1_DSM-22366_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:29,602] [INFO] Task started: fastANI
[2024-01-24 13:33:29,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg34de8df6-fa09-4a9f-822a-3ee47ad868d4/GCF_000771565.1_DSM-22366_genomic.fna.gz --refList GCF_000771565.1_DSM-22366_genomic.fna/target_genomes_gtdb.txt --output GCF_000771565.1_DSM-22366_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:44,440] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:44,455] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:44,456] [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_000741705.1	s__Bifidobacterium psychraerophilum	99.9986	842	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_000738005.1	s__Bifidobacterium crudilactis	80.7759	390	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	78.7006	125	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741285.1	s__Bifidobacterium mongoliense	78.4952	147	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_000741775.1	s__Bifidobacterium subtile	78.2922	164	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_002286915.1	s__Bifidobacterium italicum	77.8232	102	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.7874	136	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018555635.1	s__Bifidobacterium sp018555635	77.7102	125	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	77.701	135	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	77.6907	154	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	77.6691	142	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	77.6567	169	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014898155.1	s__Bifidobacterium eulemuris	77.6522	170	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009299505.1	s__Bifidobacterium ramosum	77.6278	139	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001042635.1	s__Bifidobacterium scardovii	77.5854	166	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.5828	134	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_012932675.1	s__Bifidobacterium sp012932675	77.5023	143	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042595.1	s__Bifidobacterium dentium	77.4135	139	845	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_010667615.1	s__Bifidobacterium choloepi	77.0776	118	845	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 13:33:44,457] [INFO] GTDB search result was written to GCF_000771565.1_DSM-22366_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:44,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:44,462] [INFO] DFAST_QC result json was written to GCF_000771565.1_DSM-22366_genomic.fna/dqc_result.json
[2024-01-24 13:33:44,462] [INFO] DFAST_QC completed!
[2024-01-24 13:33:44,462] [INFO] Total running time: 0h1m9s