[2023-06-27 15:01:33,059] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:01:33,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:01:33,062] [INFO] DQC Reference Directory: /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference
[2023-06-27 15:01:34,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:01:34,315] [INFO] Task started: Prodigal
[2023-06-27 15:01:34,315] [INFO] Running command: gunzip -c /var/lib/cwl/stg95082213-4c2b-4b78-b07e-ac25c5c944c5/GCA_002405085.1_ASM240508v1_genomic.fna.gz | prodigal -d GCA_002405085.1_ASM240508v1_genomic.fna/cds.fna -a GCA_002405085.1_ASM240508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:01:40,308] [INFO] Task succeeded: Prodigal
[2023-06-27 15:01:40,308] [INFO] Task started: HMMsearch
[2023-06-27 15:01:40,308] [INFO] Running command: hmmsearch --tblout GCA_002405085.1_ASM240508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/reference_markers.hmm GCA_002405085.1_ASM240508v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:01:40,533] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:01:40,536] [INFO] Found 6/6 markers.
[2023-06-27 15:01:40,556] [INFO] Query marker FASTA was written to GCA_002405085.1_ASM240508v1_genomic.fna/markers.fasta
[2023-06-27 15:01:40,557] [INFO] Task started: Blastn
[2023-06-27 15:01:40,557] [INFO] Running command: blastn -query GCA_002405085.1_ASM240508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/reference_markers.fasta -out GCA_002405085.1_ASM240508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:41,496] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:41,501] [INFO] Selected 22 target genomes.
[2023-06-27 15:01:41,502] [INFO] Target genome list was writen to GCA_002405085.1_ASM240508v1_genomic.fna/target_genomes.txt
[2023-06-27 15:01:41,511] [INFO] Task started: fastANI
[2023-06-27 15:01:41,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg95082213-4c2b-4b78-b07e-ac25c5c944c5/GCA_002405085.1_ASM240508v1_genomic.fna.gz --refList GCA_002405085.1_ASM240508v1_genomic.fna/target_genomes.txt --output GCA_002405085.1_ASM240508v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:01:51,780] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:51,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:01:51,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:01:51,800] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:01:51,800] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:01:51,800] [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 adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	83.9486	391	575	95	below_threshold
Bifidobacterium adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	83.8802	395	575	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	83.7056	397	575	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	83.6981	400	575	95	below_threshold
Bifidobacterium moukalabense	strain=GG01	GCA_005405645.1	1333651	1333651	type	True	82.7874	374	575	95	below_threshold
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	82.6278	393	575	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	82.4754	345	575	95	below_threshold
Bifidobacterium dentium	strain=DSM 20436	GCA_000771725.1	1689	1689	type	True	82.1124	364	575	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	82.0494	373	575	95	below_threshold
Bifidobacterium dentium	strain=DSM 20436	GCA_900105745.1	1689	1689	type	True	81.9738	375	575	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	81.9265	357	575	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	81.9085	362	575	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.4397	327	575	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.1373	317	575	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	81.0968	297	575	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.5798	224	575	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.6742	111	575	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	76.9993	75	575	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.1497	65	575	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:01:51,802] [INFO] DFAST Taxonomy check result was written to GCA_002405085.1_ASM240508v1_genomic.fna/tc_result.tsv
[2023-06-27 15:01:51,803] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:01:51,803] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:01:51,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/checkm_data
[2023-06-27 15:01:51,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:01:51,830] [INFO] Task started: CheckM
[2023-06-27 15:01:51,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002405085.1_ASM240508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002405085.1_ASM240508v1_genomic.fna/checkm_input GCA_002405085.1_ASM240508v1_genomic.fna/checkm_result
[2023-06-27 15:02:14,054] [INFO] Task succeeded: CheckM
[2023-06-27 15:02:14,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-27 15:02:14,089] [INFO] ===== Completeness check finished =====
[2023-06-27 15:02:14,090] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:02:14,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002405085.1_ASM240508v1_genomic.fna/markers.fasta)
[2023-06-27 15:02:14,090] [INFO] Task started: Blastn
[2023-06-27 15:02:14,090] [INFO] Running command: blastn -query GCA_002405085.1_ASM240508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803bf11d-b944-4f66-b3f5-a535506ea2ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_002405085.1_ASM240508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:02:15,368] [INFO] Task succeeded: Blastn
[2023-06-27 15:02:15,375] [INFO] Selected 12 target genomes.
[2023-06-27 15:02:15,375] [INFO] Target genome list was writen to GCA_002405085.1_ASM240508v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:02:15,386] [INFO] Task started: fastANI
[2023-06-27 15:02:15,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg95082213-4c2b-4b78-b07e-ac25c5c944c5/GCA_002405085.1_ASM240508v1_genomic.fna.gz --refList GCA_002405085.1_ASM240508v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002405085.1_ASM240508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:02:21,105] [INFO] Task succeeded: fastANI
[2023-06-27 15:02:21,116] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 15:02:21,117] [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
GCA_002451435.1	s__Bifidobacterium sp002451435	99.4659	494	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	conclusive
GCF_000010425.1	s__Bifidobacterium adolescentis	83.8802	395	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_000770925.1	s__Bifidobacterium ruminantium	83.6981	400	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_000522505.1	s__Bifidobacterium moukalabense	82.6489	392	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	82.4919	358	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_002742445.1	s__Bifidobacterium sp002742445	82.2224	348	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	82.0843	347	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_001042595.1	s__Bifidobacterium dentium	82.0068	376	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	81.9085	362	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_009299505.1	s__Bifidobacterium ramosum	81.3802	337	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018555635.1	s__Bifidobacterium sp018555635	81.1061	304	575	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	81.0284	307	575	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 15:02:21,119] [INFO] GTDB search result was written to GCA_002405085.1_ASM240508v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:02:21,120] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:02:21,124] [INFO] DFAST_QC result json was written to GCA_002405085.1_ASM240508v1_genomic.fna/dqc_result.json
[2023-06-27 15:02:21,125] [INFO] DFAST_QC completed!
[2023-06-27 15:02:21,125] [INFO] Total running time: 0h0m48s