[2023-06-13 13:51:47,294] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:51:47,297] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:51:47,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference
[2023-06-13 13:51:48,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:51:48,513] [INFO] Task started: Prodigal
[2023-06-13 13:51:48,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f36bf9b-29d6-4ce7-863d-c073ddf85b6b/GCA_022741385.1_ASM2274138v1_genomic.fna.gz | prodigal -d GCA_022741385.1_ASM2274138v1_genomic.fna/cds.fna -a GCA_022741385.1_ASM2274138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:51:55,138] [INFO] Task succeeded: Prodigal
[2023-06-13 13:51:55,139] [INFO] Task started: HMMsearch
[2023-06-13 13:51:55,139] [INFO] Running command: hmmsearch --tblout GCA_022741385.1_ASM2274138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/reference_markers.hmm GCA_022741385.1_ASM2274138v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:51:55,341] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:51:55,343] [INFO] Found 6/6 markers.
[2023-06-13 13:51:55,373] [INFO] Query marker FASTA was written to GCA_022741385.1_ASM2274138v1_genomic.fna/markers.fasta
[2023-06-13 13:51:55,374] [INFO] Task started: Blastn
[2023-06-13 13:51:55,374] [INFO] Running command: blastn -query GCA_022741385.1_ASM2274138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/reference_markers.fasta -out GCA_022741385.1_ASM2274138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:51:56,208] [INFO] Task succeeded: Blastn
[2023-06-13 13:51:56,212] [INFO] Selected 9 target genomes.
[2023-06-13 13:51:56,212] [INFO] Target genome list was writen to GCA_022741385.1_ASM2274138v1_genomic.fna/target_genomes.txt
[2023-06-13 13:51:56,213] [INFO] Task started: fastANI
[2023-06-13 13:51:56,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f36bf9b-29d6-4ce7-863d-c073ddf85b6b/GCA_022741385.1_ASM2274138v1_genomic.fna.gz --refList GCA_022741385.1_ASM2274138v1_genomic.fna/target_genomes.txt --output GCA_022741385.1_ASM2274138v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:52:00,856] [INFO] Task succeeded: fastANI
[2023-06-13 13:52:00,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:52:00,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:52:00,872] [INFO] Found 9 fastANI hits (7 hits with ANI > threshold)
[2023-06-13 13:52:00,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 13:52:00,872] [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 longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	98.1401	584	646	95	conclusive
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	98.1138	568	646	95	conclusive
Bifidobacterium longum subsp. infantis	strain=ATCC 15697	GCA_000020425.1	1682	216816	type	True	98.1045	594	646	95	conclusive
Bifidobacterium longum subsp. infantis	strain=JCM 1222	GCA_000269965.1	1682	216816	type	True	98.0994	584	646	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	95.7433	509	646	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	95.702	515	646	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	95.5791	512	646	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	94.9501	486	646	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	94.9449	487	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:52:00,875] [INFO] DFAST Taxonomy check result was written to GCA_022741385.1_ASM2274138v1_genomic.fna/tc_result.tsv
[2023-06-13 13:52:00,876] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:52:00,876] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:52:00,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/checkm_data
[2023-06-13 13:52:00,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:52:00,906] [INFO] Task started: CheckM
[2023-06-13 13:52:00,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022741385.1_ASM2274138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022741385.1_ASM2274138v1_genomic.fna/checkm_input GCA_022741385.1_ASM2274138v1_genomic.fna/checkm_result
[2023-06-13 13:52:26,069] [INFO] Task succeeded: CheckM
[2023-06-13 13:52:26,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:52:26,102] [INFO] ===== Completeness check finished =====
[2023-06-13 13:52:26,102] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:52:26,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022741385.1_ASM2274138v1_genomic.fna/markers.fasta)
[2023-06-13 13:52:26,103] [INFO] Task started: Blastn
[2023-06-13 13:52:26,103] [INFO] Running command: blastn -query GCA_022741385.1_ASM2274138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebfac0e-97c9-47aa-95fc-15b13d752c44/dqc_reference/reference_markers_gtdb.fasta -out GCA_022741385.1_ASM2274138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:52:27,348] [INFO] Task succeeded: Blastn
[2023-06-13 13:52:27,353] [INFO] Selected 9 target genomes.
[2023-06-13 13:52:27,354] [INFO] Target genome list was writen to GCA_022741385.1_ASM2274138v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:52:27,357] [INFO] Task started: fastANI
[2023-06-13 13:52:27,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f36bf9b-29d6-4ce7-863d-c073ddf85b6b/GCA_022741385.1_ASM2274138v1_genomic.fna.gz --refList GCA_022741385.1_ASM2274138v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022741385.1_ASM2274138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:52:31,864] [INFO] Task succeeded: fastANI
[2023-06-13 13:52:31,877] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:52:31,877] [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_000269965.1	s__Bifidobacterium infantis	98.0994	584	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	conclusive
GCF_000196555.1	s__Bifidobacterium longum	94.9501	486	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_001025175.1	s__Bifidobacterium breve	86.7139	460	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	83.5517	415	646	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	83.4538	423	646	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	82.8044	399	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_000741695.1	s__Bifidobacterium reuteri	82.6403	388	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_012932425.1	s__Bifidobacterium sp012932425	80.7356	324	646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:52:31,879] [INFO] GTDB search result was written to GCA_022741385.1_ASM2274138v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:52:31,880] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:52:31,883] [INFO] DFAST_QC result json was written to GCA_022741385.1_ASM2274138v1_genomic.fna/dqc_result.json
[2023-06-13 13:52:31,883] [INFO] DFAST_QC completed!
[2023-06-13 13:52:31,883] [INFO] Total running time: 0h0m45s