[2024-01-25 19:38:50,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:50,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:50,587] [INFO] DQC Reference Directory: /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference
[2024-01-25 19:38:51,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:51,749] [INFO] Task started: Prodigal
[2024-01-25 19:38:51,749] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5ae52a4-35ab-43e0-9323-9c504232b9d2/GCF_018555435.2_ASM1855543v2_genomic.fna.gz | prodigal -d GCF_018555435.2_ASM1855543v2_genomic.fna/cds.fna -a GCF_018555435.2_ASM1855543v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:00,413] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:00,413] [INFO] Task started: HMMsearch
[2024-01-25 19:39:00,413] [INFO] Running command: hmmsearch --tblout GCF_018555435.2_ASM1855543v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/reference_markers.hmm GCF_018555435.2_ASM1855543v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:00,638] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:00,639] [INFO] Found 6/6 markers.
[2024-01-25 19:39:00,665] [INFO] Query marker FASTA was written to GCF_018555435.2_ASM1855543v2_genomic.fna/markers.fasta
[2024-01-25 19:39:00,665] [INFO] Task started: Blastn
[2024-01-25 19:39:00,665] [INFO] Running command: blastn -query GCF_018555435.2_ASM1855543v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/reference_markers.fasta -out GCF_018555435.2_ASM1855543v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:01,659] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:01,662] [INFO] Selected 12 target genomes.
[2024-01-25 19:39:01,662] [INFO] Target genome list was writen to GCF_018555435.2_ASM1855543v2_genomic.fna/target_genomes.txt
[2024-01-25 19:39:01,678] [INFO] Task started: fastANI
[2024-01-25 19:39:01,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ae52a4-35ab-43e0-9323-9c504232b9d2/GCF_018555435.2_ASM1855543v2_genomic.fna.gz --refList GCF_018555435.2_ASM1855543v2_genomic.fna/target_genomes.txt --output GCF_018555435.2_ASM1855543v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:09,996] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:09,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:09,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:10,005] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:10,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:10,005] [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 amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	100.0	1030	1047	95	conclusive
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	90.9477	750	1047	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000771645.1	762212	762212	type	True	90.868	766	1047	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	90.7747	759	1047	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	87.0427	651	1047	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	86.7432	661	1047	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	86.6572	608	1047	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	84.7886	528	1047	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.2937	526	1047	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.2552	318	1047	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.9384	154	1047	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.888	169	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:10,006] [INFO] DFAST Taxonomy check result was written to GCF_018555435.2_ASM1855543v2_genomic.fna/tc_result.tsv
[2024-01-25 19:39:10,007] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:10,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:10,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/checkm_data
[2024-01-25 19:39:10,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:10,045] [INFO] Task started: CheckM
[2024-01-25 19:39:10,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018555435.2_ASM1855543v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018555435.2_ASM1855543v2_genomic.fna/checkm_input GCF_018555435.2_ASM1855543v2_genomic.fna/checkm_result
[2024-01-25 19:39:38,958] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:38,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:38,974] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:38,975] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:38,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018555435.2_ASM1855543v2_genomic.fna/markers.fasta)
[2024-01-25 19:39:38,975] [INFO] Task started: Blastn
[2024-01-25 19:39:38,975] [INFO] Running command: blastn -query GCF_018555435.2_ASM1855543v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge347839c-7f99-4694-95e3-eb3d5b0d6715/dqc_reference/reference_markers_gtdb.fasta -out GCF_018555435.2_ASM1855543v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:40,539] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:40,542] [INFO] Selected 9 target genomes.
[2024-01-25 19:39:40,542] [INFO] Target genome list was writen to GCF_018555435.2_ASM1855543v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:40,548] [INFO] Task started: fastANI
[2024-01-25 19:39:40,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ae52a4-35ab-43e0-9323-9c504232b9d2/GCF_018555435.2_ASM1855543v2_genomic.fna.gz --refList GCF_018555435.2_ASM1855543v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018555435.2_ASM1855543v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:46,749] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:46,755] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:39:46,756] [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_000741165.1	s__Bifidobacterium biavatii	90.7802	759	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555335.1	s__Bifidobacterium sp018555335	86.8632	646	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	86.7681	655	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	86.6098	610	1047	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	84.9878	580	1047	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	84.7653	529	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	84.0848	563	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555635.1	s__Bifidobacterium sp018555635	83.9972	518	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	82.5823	445	1047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:46,757] [INFO] GTDB search result was written to GCF_018555435.2_ASM1855543v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:46,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:46,760] [INFO] DFAST_QC result json was written to GCF_018555435.2_ASM1855543v2_genomic.fna/dqc_result.json
[2024-01-25 19:39:46,760] [INFO] DFAST_QC completed!
[2024-01-25 19:39:46,760] [INFO] Total running time: 0h0m56s