[2024-01-25 17:51:35,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference
[2024-01-25 17:51:36,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,622] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg240073c1-1200-4993-83ea-28883b2de0d3/GCF_010667665.1_ASM1066766v1_genomic.fna.gz | prodigal -d GCF_010667665.1_ASM1066766v1_genomic.fna/cds.fna -a GCF_010667665.1_ASM1066766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:45,088] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:45,088] [INFO] Task started: HMMsearch
[2024-01-25 17:51:45,088] [INFO] Running command: hmmsearch --tblout GCF_010667665.1_ASM1066766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/reference_markers.hmm GCF_010667665.1_ASM1066766v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:45,284] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:45,285] [INFO] Found 6/6 markers.
[2024-01-25 17:51:45,309] [INFO] Query marker FASTA was written to GCF_010667665.1_ASM1066766v1_genomic.fna/markers.fasta
[2024-01-25 17:51:45,309] [INFO] Task started: Blastn
[2024-01-25 17:51:45,309] [INFO] Running command: blastn -query GCF_010667665.1_ASM1066766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/reference_markers.fasta -out GCF_010667665.1_ASM1066766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:46,215] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:46,218] [INFO] Selected 13 target genomes.
[2024-01-25 17:51:46,219] [INFO] Target genome list was writen to GCF_010667665.1_ASM1066766v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:46,230] [INFO] Task started: fastANI
[2024-01-25 17:51:46,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg240073c1-1200-4993-83ea-28883b2de0d3/GCF_010667665.1_ASM1066766v1_genomic.fna.gz --refList GCF_010667665.1_ASM1066766v1_genomic.fna/target_genomes.txt --output GCF_010667665.1_ASM1066766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:55,192] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:55,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:55,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:55,202] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:55,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:55,202] [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 ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	100.0	994	999	95	conclusive
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	99.9917	986	999	95	conclusive
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	88.466	715	999	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	87.9293	689	999	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	87.3076	674	999	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	86.9733	671	999	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	86.8719	650	999	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	84.1057	559	999	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	83.9648	581	999	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.638	535	999	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.2354	309	999	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.1841	137	999	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	76.1602	110	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:55,204] [INFO] DFAST Taxonomy check result was written to GCF_010667665.1_ASM1066766v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:55,205] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:55,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:55,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/checkm_data
[2024-01-25 17:51:55,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:55,244] [INFO] Task started: CheckM
[2024-01-25 17:51:55,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010667665.1_ASM1066766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010667665.1_ASM1066766v1_genomic.fna/checkm_input GCF_010667665.1_ASM1066766v1_genomic.fna/checkm_result
[2024-01-25 17:52:24,487] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:24,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:24,511] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:24,511] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:24,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010667665.1_ASM1066766v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:24,513] [INFO] Task started: Blastn
[2024-01-25 17:52:24,513] [INFO] Running command: blastn -query GCF_010667665.1_ASM1066766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4797da8f-027d-4b7f-b91d-f9d09b0b346d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010667665.1_ASM1066766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:25,948] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:25,951] [INFO] Selected 8 target genomes.
[2024-01-25 17:52:25,951] [INFO] Target genome list was writen to GCF_010667665.1_ASM1066766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:26,004] [INFO] Task started: fastANI
[2024-01-25 17:52:26,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg240073c1-1200-4993-83ea-28883b2de0d3/GCF_010667665.1_ASM1066766v1_genomic.fna.gz --refList GCF_010667665.1_ASM1066766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010667665.1_ASM1066766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:32,048] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:32,054] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:32,055] [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_009299505.1	s__Bifidobacterium ramosum	99.9917	986	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_018555335.1	s__Bifidobacterium sp018555335	88.7688	701	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	87.9487	688	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	87.0007	669	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	84.2569	567	999	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	83.9847	581	999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003952945.1	s__Bifidobacterium samirii	83.8486	521	999	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	82.4514	464	999	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 17:52:32,056] [INFO] GTDB search result was written to GCF_010667665.1_ASM1066766v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:32,056] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:32,059] [INFO] DFAST_QC result json was written to GCF_010667665.1_ASM1066766v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:32,059] [INFO] DFAST_QC completed!
[2024-01-25 17:52:32,059] [INFO] Total running time: 0h0m57s