[2023-06-08 12:26:33,133] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:33,140] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:33,142] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference
[2023-06-08 12:26:34,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:34,550] [INFO] Task started: Prodigal
[2023-06-08 12:26:34,551] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc2898a7-8c7f-4d7b-9ed6-ed59794fc75e/GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:39,850] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:39,850] [INFO] Task started: HMMsearch
[2023-06-08 12:26:39,850] [INFO] Running command: hmmsearch --tblout GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/reference_markers.hmm GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:40,085] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:40,086] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbc2898a7-8c7f-4d7b-9ed6-ed59794fc75e/GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:26:40,109] [INFO] Query marker FASTA was written to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:26:40,109] [INFO] Task started: Blastn
[2023-06-08 12:26:40,109] [INFO] Running command: blastn -query GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/reference_markers.fasta -out GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:41,013] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:41,018] [INFO] Selected 13 target genomes.
[2023-06-08 12:26:41,018] [INFO] Target genome list was writen to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:26:41,028] [INFO] Task started: fastANI
[2023-06-08 12:26:41,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2898a7-8c7f-4d7b-9ed6-ed59794fc75e/GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:26:47,057] [INFO] Task succeeded: fastANI
[2023-06-08 12:26:47,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:26:47,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:26:47,067] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2023-06-08 12:26:47,067] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 12:26:47,067] [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 boum	strain=LMG 10736	GCA_000741535.1	78343	78343	type	True	97.6496	446	481	95	conclusive
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	97.6421	449	481	95	conclusive
Bifidobacterium boum	strain=DSM 20432	GCA_000687615.1	78343	78343	type	True	97.6338	447	481	95	conclusive
Bifidobacterium porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	85.6427	382	481	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	84.9787	373	481	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	84.9528	373	481	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.1492	172	481	95	below_threshold
Bifidobacterium adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	78.9299	180	481	95	below_threshold
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	78.9246	178	481	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.8575	129	481	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:26:47,108] [INFO] DFAST Taxonomy check result was written to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:26:47,109] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:26:47,109] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:26:47,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/checkm_data
[2023-06-08 12:26:47,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:26:47,134] [INFO] Task started: CheckM
[2023-06-08 12:26:47,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:27:10,315] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:10,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.06%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:10,338] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:10,338] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:10,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:27:10,339] [INFO] Task started: Blastn
[2023-06-08 12:27:10,339] [INFO] Running command: blastn -query GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b6d5bd-cffe-4354-a8cf-7db783536aeb/dqc_reference/reference_markers_gtdb.fasta -out GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:11,721] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:11,732] [INFO] Selected 13 target genomes.
[2023-06-08 12:27:11,732] [INFO] Target genome list was writen to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:11,799] [INFO] Task started: fastANI
[2023-06-08 12:27:11,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc2898a7-8c7f-4d7b-9ed6-ed59794fc75e/GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:17,981] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:18,001] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:18,001] [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_000741535.1	s__Bifidobacterium boum	97.6496	446	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	conclusive
GCA_000741495.1	s__Bifidobacterium thermophilum_A	94.7786	441	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000771265.1	s__Bifidobacterium thermophilum	85.6341	384	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_009299485.1	s__Bifidobacterium apri	85.2857	388	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.1489	167	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	78.9362	175	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010425.1	s__Bifidobacterium adolescentis	78.9299	180	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_001042635.1	s__Bifidobacterium scardovii	78.837	179	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCA_002451435.1	s__Bifidobacterium sp002451435	78.8078	140	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	78.7918	159	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_014898175.1	s__Bifidobacterium lemurum	78.7073	163	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003952945.1	s__Bifidobacterium samirii	78.6595	159	481	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	78.5664	142	481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:18,003] [INFO] GTDB search result was written to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:18,004] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:18,008] [INFO] DFAST_QC result json was written to GCA_945830665.1_SRR5240749_bin.1_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:27:18,009] [INFO] DFAST_QC completed!
[2023-06-08 12:27:18,009] [INFO] Total running time: 0h0m45s