[2024-01-24 14:14:47,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference
[2024-01-24 14:14:49,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,424] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dc58340-5e58-4f13-9da3-9ef8b22fe65e/GCF_019331695.1_ASM1933169v1_genomic.fna.gz | prodigal -d GCF_019331695.1_ASM1933169v1_genomic.fna/cds.fna -a GCF_019331695.1_ASM1933169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:58,744] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:58,744] [INFO] Task started: HMMsearch
[2024-01-24 14:14:58,744] [INFO] Running command: hmmsearch --tblout GCF_019331695.1_ASM1933169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/reference_markers.hmm GCF_019331695.1_ASM1933169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:58,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:58,979] [INFO] Found 6/6 markers.
[2024-01-24 14:14:59,007] [INFO] Query marker FASTA was written to GCF_019331695.1_ASM1933169v1_genomic.fna/markers.fasta
[2024-01-24 14:14:59,007] [INFO] Task started: Blastn
[2024-01-24 14:14:59,008] [INFO] Running command: blastn -query GCF_019331695.1_ASM1933169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/reference_markers.fasta -out GCF_019331695.1_ASM1933169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:00,075] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:00,079] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:00,080] [INFO] Target genome list was writen to GCF_019331695.1_ASM1933169v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:00,170] [INFO] Task started: fastANI
[2024-01-24 14:15:00,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc58340-5e58-4f13-9da3-9ef8b22fe65e/GCF_019331695.1_ASM1933169v1_genomic.fna.gz --refList GCF_019331695.1_ASM1933169v1_genomic.fna/target_genomes.txt --output GCF_019331695.1_ASM1933169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:08,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:08,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:08,281] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:08,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:08,281] [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 pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	100.0	872	873	95	conclusive
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	89.0732	684	873	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	88.6879	698	873	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	88.4054	657	873	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	83.9916	563	873	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	83.8967	601	873	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	82.0581	406	873	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.8207	381	873	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.7498	412	873	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.5487	250	873	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5125	116	873	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4046	111	873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,282] [INFO] DFAST Taxonomy check result was written to GCF_019331695.1_ASM1933169v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:08,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:08,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:08,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/checkm_data
[2024-01-24 14:15:08,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:08,311] [INFO] Task started: CheckM
[2024-01-24 14:15:08,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019331695.1_ASM1933169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019331695.1_ASM1933169v1_genomic.fna/checkm_input GCF_019331695.1_ASM1933169v1_genomic.fna/checkm_result
[2024-01-24 14:15:38,680] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:38,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:38,700] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:38,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:38,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019331695.1_ASM1933169v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:38,701] [INFO] Task started: Blastn
[2024-01-24 14:15:38,701] [INFO] Running command: blastn -query GCF_019331695.1_ASM1933169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg512406b5-4674-4675-9bfc-a8f46afb1f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_019331695.1_ASM1933169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:40,237] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:40,246] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:40,247] [INFO] Target genome list was writen to GCF_019331695.1_ASM1933169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:40,260] [INFO] Task started: fastANI
[2024-01-24 14:15:40,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc58340-5e58-4f13-9da3-9ef8b22fe65e/GCF_019331695.1_ASM1933169v1_genomic.fna.gz --refList GCF_019331695.1_ASM1933169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019331695.1_ASM1933169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:47,580] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:47,600] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:47,600] [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_010667655.1	s__Galliscardovia saimiriisciurei	89.0739	684	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002802875.1	s__Galliscardovia primatium	88.6618	700	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129925.1	s__Galliscardovia catulorum	88.3673	659	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	84.2949	556	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_003952005.1	s__Galliscardovia callimiconis	84.021	561	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_002234915.1	s__Galliscardovia vansinderenii	83.8967	601	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259645.1	s__Galliscardovia tissieri	83.0161	532	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.5487	412	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	82.2533	440	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	82.0423	414	873	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	81.7916	393	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698145.1	s__Bifidobacterium vespertilionis	81.106	398	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:47,602] [INFO] GTDB search result was written to GCF_019331695.1_ASM1933169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:47,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:47,607] [INFO] DFAST_QC result json was written to GCF_019331695.1_ASM1933169v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:47,607] [INFO] DFAST_QC completed!
[2024-01-24 14:15:47,607] [INFO] Total running time: 0h1m0s