[2023-06-13 00:45:20,883] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:20,889] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:20,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference
[2023-06-13 00:45:22,129] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:22,130] [INFO] Task started: Prodigal
[2023-06-13 00:45:22,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg06fa5f62-a3df-47c3-8e83-51577fbb61d0/GCA_022720695.1_ASM2272069v1_genomic.fna.gz | prodigal -d GCA_022720695.1_ASM2272069v1_genomic.fna/cds.fna -a GCA_022720695.1_ASM2272069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:30,300] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:30,300] [INFO] Task started: HMMsearch
[2023-06-13 00:45:30,300] [INFO] Running command: hmmsearch --tblout GCA_022720695.1_ASM2272069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/reference_markers.hmm GCA_022720695.1_ASM2272069v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:30,579] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:30,580] [INFO] Found 6/6 markers.
[2023-06-13 00:45:30,605] [INFO] Query marker FASTA was written to GCA_022720695.1_ASM2272069v1_genomic.fna/markers.fasta
[2023-06-13 00:45:30,606] [INFO] Task started: Blastn
[2023-06-13 00:45:30,606] [INFO] Running command: blastn -query GCA_022720695.1_ASM2272069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/reference_markers.fasta -out GCA_022720695.1_ASM2272069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:31,606] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:31,609] [INFO] Selected 11 target genomes.
[2023-06-13 00:45:31,610] [INFO] Target genome list was writen to GCA_022720695.1_ASM2272069v1_genomic.fna/target_genomes.txt
[2023-06-13 00:45:31,611] [INFO] Task started: fastANI
[2023-06-13 00:45:31,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg06fa5f62-a3df-47c3-8e83-51577fbb61d0/GCA_022720695.1_ASM2272069v1_genomic.fna.gz --refList GCA_022720695.1_ASM2272069v1_genomic.fna/target_genomes.txt --output GCA_022720695.1_ASM2272069v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:37,825] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:37,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:37,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:37,836] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 00:45:37,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:45:37,837] [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=DSM 20088	GCA_000771105.1	1682	216816	type	True	98.2825	669	794	95	conclusive
Bifidobacterium longum subsp. infantis	strain=JCM 1222	GCA_000269965.1	1682	216816	type	True	98.231	716	794	95	conclusive
Bifidobacterium longum subsp. infantis	strain=ATCC 15697	GCA_000020425.1	1682	216816	type	True	98.222	713	794	95	conclusive
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	98.1962	717	794	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	95.71	583	794	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	94.9924	559	794	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	84.1013	480	794	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.384	401	794	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.9025	144	794	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	75.8865	54	794	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	75.7076	56	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:45:37,839] [INFO] DFAST Taxonomy check result was written to GCA_022720695.1_ASM2272069v1_genomic.fna/tc_result.tsv
[2023-06-13 00:45:37,840] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:37,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:37,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/checkm_data
[2023-06-13 00:45:37,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:37,868] [INFO] Task started: CheckM
[2023-06-13 00:45:37,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720695.1_ASM2272069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720695.1_ASM2272069v1_genomic.fna/checkm_input GCA_022720695.1_ASM2272069v1_genomic.fna/checkm_result
[2023-06-13 00:46:07,796] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:07,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:46:07,854] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:07,855] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:07,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720695.1_ASM2272069v1_genomic.fna/markers.fasta)
[2023-06-13 00:46:07,856] [INFO] Task started: Blastn
[2023-06-13 00:46:07,856] [INFO] Running command: blastn -query GCA_022720695.1_ASM2272069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92a6bd5e-b9d3-4702-b766-f987b621d76b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720695.1_ASM2272069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:09,204] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:09,209] [INFO] Selected 8 target genomes.
[2023-06-13 00:46:09,209] [INFO] Target genome list was writen to GCA_022720695.1_ASM2272069v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:09,211] [INFO] Task started: fastANI
[2023-06-13 00:46:09,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg06fa5f62-a3df-47c3-8e83-51577fbb61d0/GCA_022720695.1_ASM2272069v1_genomic.fna.gz --refList GCA_022720695.1_ASM2272069v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720695.1_ASM2272069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:13,756] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:13,764] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:46:13,764] [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	98.1982	717	794	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	94.9924	559	794	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	87.419	537	794	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	84.0432	487	794	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	83.9594	497	794	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	83.3228	466	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.1839	392	794	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 00:46:13,766] [INFO] GTDB search result was written to GCA_022720695.1_ASM2272069v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:13,767] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:13,770] [INFO] DFAST_QC result json was written to GCA_022720695.1_ASM2272069v1_genomic.fna/dqc_result.json
[2023-06-13 00:46:13,771] [INFO] DFAST_QC completed!
[2023-06-13 00:46:13,771] [INFO] Total running time: 0h0m53s