[2023-06-16 19:45:44,217] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:45:44,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:45:44,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference
[2023-06-16 19:45:45,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:45:45,380] [INFO] Task started: Prodigal
[2023-06-16 19:45:45,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgf22fc6b5-b028-4f54-a1dc-a6296b35fabd/GCA_003531035.1_ASM353103v1_genomic.fna.gz | prodigal -d GCA_003531035.1_ASM353103v1_genomic.fna/cds.fna -a GCA_003531035.1_ASM353103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:45:50,469] [INFO] Task succeeded: Prodigal
[2023-06-16 19:45:50,469] [INFO] Task started: HMMsearch
[2023-06-16 19:45:50,469] [INFO] Running command: hmmsearch --tblout GCA_003531035.1_ASM353103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/reference_markers.hmm GCA_003531035.1_ASM353103v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:45:50,630] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:45:50,631] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf22fc6b5-b028-4f54-a1dc-a6296b35fabd/GCA_003531035.1_ASM353103v1_genomic.fna.gz]
[2023-06-16 19:45:50,651] [INFO] Query marker FASTA was written to GCA_003531035.1_ASM353103v1_genomic.fna/markers.fasta
[2023-06-16 19:45:50,652] [INFO] Task started: Blastn
[2023-06-16 19:45:50,652] [INFO] Running command: blastn -query GCA_003531035.1_ASM353103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/reference_markers.fasta -out GCA_003531035.1_ASM353103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:45:51,491] [INFO] Task succeeded: Blastn
[2023-06-16 19:45:51,495] [INFO] Selected 8 target genomes.
[2023-06-16 19:45:51,495] [INFO] Target genome list was writen to GCA_003531035.1_ASM353103v1_genomic.fna/target_genomes.txt
[2023-06-16 19:45:51,498] [INFO] Task started: fastANI
[2023-06-16 19:45:51,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22fc6b5-b028-4f54-a1dc-a6296b35fabd/GCA_003531035.1_ASM353103v1_genomic.fna.gz --refList GCA_003531035.1_ASM353103v1_genomic.fna/target_genomes.txt --output GCA_003531035.1_ASM353103v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:45:54,877] [INFO] Task succeeded: fastANI
[2023-06-16 19:45:54,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:45:54,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:45:54,886] [INFO] Found 8 fastANI hits (8 hits with ANI > threshold)
[2023-06-16 19:45:54,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 19:45:54,887] [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. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	98.7018	491	521	95	conclusive
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	98.6884	487	521	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	98.6859	485	521	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	98.6852	485	521	95	conclusive
Bifidobacterium longum subsp. longum	strain=LMG 13197	GCA_000741245.1	1679	216816	type	True	98.6762	487	521	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	96.0971	451	521	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	96.002	446	521	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	95.9282	447	521	95	conclusive
--------------------------------------------------------------------------------
[2023-06-16 19:45:54,888] [INFO] DFAST Taxonomy check result was written to GCA_003531035.1_ASM353103v1_genomic.fna/tc_result.tsv
[2023-06-16 19:45:54,889] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:45:54,889] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:45:54,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/checkm_data
[2023-06-16 19:45:54,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:45:54,911] [INFO] Task started: CheckM
[2023-06-16 19:45:54,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003531035.1_ASM353103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003531035.1_ASM353103v1_genomic.fna/checkm_input GCA_003531035.1_ASM353103v1_genomic.fna/checkm_result
[2023-06-16 19:46:14,839] [INFO] Task succeeded: CheckM
[2023-06-16 19:46:14,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.39%
Contamintation: 3.03%
Strain heterogeneity: 87.50%
--------------------------------------------------------------------------------
[2023-06-16 19:46:14,861] [INFO] ===== Completeness check finished =====
[2023-06-16 19:46:14,861] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:46:14,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003531035.1_ASM353103v1_genomic.fna/markers.fasta)
[2023-06-16 19:46:14,861] [INFO] Task started: Blastn
[2023-06-16 19:46:14,862] [INFO] Running command: blastn -query GCA_003531035.1_ASM353103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg498d1172-072f-4bc3-841f-9dd38addbd9f/dqc_reference/reference_markers_gtdb.fasta -out GCA_003531035.1_ASM353103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:46:16,064] [INFO] Task succeeded: Blastn
[2023-06-16 19:46:16,070] [INFO] Selected 10 target genomes.
[2023-06-16 19:46:16,071] [INFO] Target genome list was writen to GCA_003531035.1_ASM353103v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:46:16,081] [INFO] Task started: fastANI
[2023-06-16 19:46:16,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22fc6b5-b028-4f54-a1dc-a6296b35fabd/GCA_003531035.1_ASM353103v1_genomic.fna.gz --refList GCA_003531035.1_ASM353103v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003531035.1_ASM353103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:46:21,028] [INFO] Task succeeded: fastANI
[2023-06-16 19:46:21,037] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:46:21,037] [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_000196555.1	s__Bifidobacterium longum	98.6859	485	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	conclusive
GCF_000269965.1	s__Bifidobacterium infantis	94.7057	427	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_001025175.1	s__Bifidobacterium breve	85.944	378	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_018555355.1	s__Bifidobacterium sp018555355	83.9241	381	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	83.6326	384	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	83.0528	356	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_009193305.1	s__Bifidobacterium cebidarum	82.572	319	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555455.1	s__Bifidobacterium sp018555455	82.2174	340	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.0239	301	521	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:46:21,039] [INFO] GTDB search result was written to GCA_003531035.1_ASM353103v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:46:21,040] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:46:21,042] [INFO] DFAST_QC result json was written to GCA_003531035.1_ASM353103v1_genomic.fna/dqc_result.json
[2023-06-16 19:46:21,043] [INFO] DFAST_QC completed!
[2023-06-16 19:46:21,043] [INFO] Total running time: 0h0m37s