[2024-01-25 18:39:50,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,765] [INFO] DQC Reference Directory: /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference
[2024-01-25 18:39:51,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,955] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg906c1812-553b-4a16-ae7f-cab9df467bd9/GCF_000741685.1_Bifpsetum_genomic.fna.gz | prodigal -d GCF_000741685.1_Bifpsetum_genomic.fna/cds.fna -a GCF_000741685.1_Bifpsetum_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:58,978] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:58,979] [INFO] Task started: HMMsearch
[2024-01-25 18:39:58,979] [INFO] Running command: hmmsearch --tblout GCF_000741685.1_Bifpsetum_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/reference_markers.hmm GCF_000741685.1_Bifpsetum_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:59,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:59,148] [INFO] Found 6/6 markers.
[2024-01-25 18:39:59,167] [INFO] Query marker FASTA was written to GCF_000741685.1_Bifpsetum_genomic.fna/markers.fasta
[2024-01-25 18:39:59,167] [INFO] Task started: Blastn
[2024-01-25 18:39:59,167] [INFO] Running command: blastn -query GCF_000741685.1_Bifpsetum_genomic.fna/markers.fasta -db /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/reference_markers.fasta -out GCF_000741685.1_Bifpsetum_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:59,959] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:59,968] [INFO] Selected 12 target genomes.
[2024-01-25 18:39:59,968] [INFO] Target genome list was writen to GCF_000741685.1_Bifpsetum_genomic.fna/target_genomes.txt
[2024-01-25 18:40:00,006] [INFO] Task started: fastANI
[2024-01-25 18:40:00,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg906c1812-553b-4a16-ae7f-cab9df467bd9/GCF_000741685.1_Bifpsetum_genomic.fna.gz --refList GCF_000741685.1_Bifpsetum_genomic.fna/target_genomes.txt --output GCF_000741685.1_Bifpsetum_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:05,740] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:05,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:05,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:05,748] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:40:05,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:05,749] [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 pseudocatenulatum	strain=LMG 10505	GCA_000741685.1	28026	28026	type	True	100.0	756	756	95	conclusive
Bifidobacterium pseudocatenulatum	strain=JCM 1200	GCA_001025215.1	28026	28026	type	True	99.9745	753	756	95	conclusive
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	99.9696	737	756	95	conclusive
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000173435.1	28026	28026	type	True	99.9664	749	756	95	conclusive
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	92.6593	562	756	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	92.6115	538	756	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	92.2512	612	756	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.0302	304	756	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.8291	222	756	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	78.0785	90	756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:05,751] [INFO] DFAST Taxonomy check result was written to GCF_000741685.1_Bifpsetum_genomic.fna/tc_result.tsv
[2024-01-25 18:40:05,752] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:05,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:05,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/checkm_data
[2024-01-25 18:40:05,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:05,785] [INFO] Task started: CheckM
[2024-01-25 18:40:05,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741685.1_Bifpsetum_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741685.1_Bifpsetum_genomic.fna/checkm_input GCF_000741685.1_Bifpsetum_genomic.fna/checkm_result
[2024-01-25 18:40:30,264] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:30,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:30,280] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:30,281] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:30,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741685.1_Bifpsetum_genomic.fna/markers.fasta)
[2024-01-25 18:40:30,282] [INFO] Task started: Blastn
[2024-01-25 18:40:30,282] [INFO] Running command: blastn -query GCF_000741685.1_Bifpsetum_genomic.fna/markers.fasta -db /var/lib/cwl/stgc255d028-750a-4e6f-b9ad-af55fd6c4a3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741685.1_Bifpsetum_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:31,469] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:31,472] [INFO] Selected 5 target genomes.
[2024-01-25 18:40:31,472] [INFO] Target genome list was writen to GCF_000741685.1_Bifpsetum_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:31,476] [INFO] Task started: fastANI
[2024-01-25 18:40:31,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg906c1812-553b-4a16-ae7f-cab9df467bd9/GCF_000741685.1_Bifpsetum_genomic.fna.gz --refList GCF_000741685.1_Bifpsetum_genomic.fna/target_genomes_gtdb.txt --output GCF_000741685.1_Bifpsetum_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:34,441] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:34,446] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:34,446] [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_001025215.1	s__Bifidobacterium pseudocatenulatum	99.9745	753	756	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	conclusive
GCF_001025195.1	s__Bifidobacterium catenulatum	92.6828	578	756	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	92.4831	598	756	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_002742445.1	s__Bifidobacterium sp002742445	92.4154	596	756	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	92.3676	612	756	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:34,448] [INFO] GTDB search result was written to GCF_000741685.1_Bifpsetum_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:34,449] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:34,451] [INFO] DFAST_QC result json was written to GCF_000741685.1_Bifpsetum_genomic.fna/dqc_result.json
[2024-01-25 18:40:34,452] [INFO] DFAST_QC completed!
[2024-01-25 18:40:34,452] [INFO] Total running time: 0h0m44s