[2023-06-30 05:02:09,895] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:02:09,897] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:02:09,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference
[2023-06-30 05:02:11,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:02:11,415] [INFO] Task started: Prodigal
[2023-06-30 05:02:11,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg2938c3b9-b4d4-460b-a634-fa6f7b349c9b/GCA_025291265.1_ASM2529126v1_genomic.fna.gz | prodigal -d GCA_025291265.1_ASM2529126v1_genomic.fna/cds.fna -a GCA_025291265.1_ASM2529126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:02:15,124] [INFO] Task succeeded: Prodigal
[2023-06-30 05:02:15,124] [INFO] Task started: HMMsearch
[2023-06-30 05:02:15,124] [INFO] Running command: hmmsearch --tblout GCA_025291265.1_ASM2529126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/reference_markers.hmm GCA_025291265.1_ASM2529126v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:02:15,370] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:02:15,372] [INFO] Found 6/6 markers.
[2023-06-30 05:02:15,390] [INFO] Query marker FASTA was written to GCA_025291265.1_ASM2529126v1_genomic.fna/markers.fasta
[2023-06-30 05:02:15,391] [INFO] Task started: Blastn
[2023-06-30 05:02:15,391] [INFO] Running command: blastn -query GCA_025291265.1_ASM2529126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/reference_markers.fasta -out GCA_025291265.1_ASM2529126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:02:16,261] [INFO] Task succeeded: Blastn
[2023-06-30 05:02:16,265] [INFO] Selected 6 target genomes.
[2023-06-30 05:02:16,265] [INFO] Target genome list was writen to GCA_025291265.1_ASM2529126v1_genomic.fna/target_genomes.txt
[2023-06-30 05:02:16,266] [INFO] Task started: fastANI
[2023-06-30 05:02:16,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg2938c3b9-b4d4-460b-a634-fa6f7b349c9b/GCA_025291265.1_ASM2529126v1_genomic.fna.gz --refList GCA_025291265.1_ASM2529126v1_genomic.fna/target_genomes.txt --output GCA_025291265.1_ASM2529126v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:02:18,702] [INFO] Task succeeded: fastANI
[2023-06-30 05:02:18,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:02:18,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:02:18,710] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:02:18,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:02:18,711] [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 mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	92.0224	296	368	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	91.9606	326	368	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	91.7916	296	368	95	below_threshold
Bifidobacterium polysaccharolyticum	strain=W8117	GCA_016101585.1	2750967	2750967	type	True	91.146	310	368	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	91.0138	308	368	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	91.0105	317	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:02:18,713] [INFO] DFAST Taxonomy check result was written to GCA_025291265.1_ASM2529126v1_genomic.fna/tc_result.tsv
[2023-06-30 05:02:18,717] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:02:18,718] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:02:18,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/checkm_data
[2023-06-30 05:02:18,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:02:18,745] [INFO] Task started: CheckM
[2023-06-30 05:02:18,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025291265.1_ASM2529126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025291265.1_ASM2529126v1_genomic.fna/checkm_input GCA_025291265.1_ASM2529126v1_genomic.fna/checkm_result
[2023-06-30 05:02:37,502] [INFO] Task succeeded: CheckM
[2023-06-30 05:02:37,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.44%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 05:02:37,527] [INFO] ===== Completeness check finished =====
[2023-06-30 05:02:37,527] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:02:37,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025291265.1_ASM2529126v1_genomic.fna/markers.fasta)
[2023-06-30 05:02:37,528] [INFO] Task started: Blastn
[2023-06-30 05:02:37,528] [INFO] Running command: blastn -query GCA_025291265.1_ASM2529126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb051a23f-fc9e-42e1-b420-623631e6f102/dqc_reference/reference_markers_gtdb.fasta -out GCA_025291265.1_ASM2529126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:02:38,651] [INFO] Task succeeded: Blastn
[2023-06-30 05:02:38,655] [INFO] Selected 10 target genomes.
[2023-06-30 05:02:38,655] [INFO] Target genome list was writen to GCA_025291265.1_ASM2529126v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:02:38,659] [INFO] Task started: fastANI
[2023-06-30 05:02:38,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg2938c3b9-b4d4-460b-a634-fa6f7b349c9b/GCA_025291265.1_ASM2529126v1_genomic.fna.gz --refList GCA_025291265.1_ASM2529126v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025291265.1_ASM2529126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:02:42,793] [INFO] Task succeeded: fastANI
[2023-06-30 05:02:42,802] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:02:42,802] [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_000499285.1	s__Bifidobacterium sp000499285	92.4691	319	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	92.1076	318	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	92.0414	308	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016100725.1	s__Bifidobacterium sp016100725	91.9662	323	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_000499185.1	s__Bifidobacterium sp000499185	91.9045	292	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	-
GCF_000967185.1	s__Bifidobacterium asteroides_B	91.8739	292	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_003202695.1	s__Bifidobacterium asteroides_G	91.2778	310	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202715.1	s__Bifidobacterium asteroides_E	91.1301	315	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	-
GCF_002715865.1	s__Bifidobacterium asteroides	91.0105	317	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	90.8071	301	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:02:42,804] [INFO] GTDB search result was written to GCA_025291265.1_ASM2529126v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:02:42,805] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:02:42,810] [INFO] DFAST_QC result json was written to GCA_025291265.1_ASM2529126v1_genomic.fna/dqc_result.json
[2023-06-30 05:02:42,810] [INFO] DFAST_QC completed!
[2023-06-30 05:02:42,810] [INFO] Total running time: 0h0m33s