[2024-01-24 13:17:41,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference
[2024-01-24 13:17:43,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:43,115] [INFO] Task started: Prodigal
[2024-01-24 13:17:43,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg99e52fe9-81c6-4c10-a66f-103e847faaba/GCF_020884755.1_ASM2088475v1_genomic.fna.gz | prodigal -d GCF_020884755.1_ASM2088475v1_genomic.fna/cds.fna -a GCF_020884755.1_ASM2088475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:49,463] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:49,464] [INFO] Task started: HMMsearch
[2024-01-24 13:17:49,464] [INFO] Running command: hmmsearch --tblout GCF_020884755.1_ASM2088475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/reference_markers.hmm GCF_020884755.1_ASM2088475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:49,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:49,719] [INFO] Found 6/6 markers.
[2024-01-24 13:17:49,740] [INFO] Query marker FASTA was written to GCF_020884755.1_ASM2088475v1_genomic.fna/markers.fasta
[2024-01-24 13:17:49,741] [INFO] Task started: Blastn
[2024-01-24 13:17:49,741] [INFO] Running command: blastn -query GCF_020884755.1_ASM2088475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/reference_markers.fasta -out GCF_020884755.1_ASM2088475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:50,611] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:50,615] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:50,616] [INFO] Target genome list was writen to GCF_020884755.1_ASM2088475v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:50,694] [INFO] Task started: fastANI
[2024-01-24 13:17:50,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e52fe9-81c6-4c10-a66f-103e847faaba/GCF_020884755.1_ASM2088475v1_genomic.fna.gz --refList GCF_020884755.1_ASM2088475v1_genomic.fna/target_genomes.txt --output GCF_020884755.1_ASM2088475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:55,788] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:55,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:55,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:55,797] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:55,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:55,798] [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	100.0	688	688	95	conclusive
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	94.0491	607	688	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	91.6631	548	688	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	91.3636	535	688	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	91.1332	575	688	95	below_threshold
Bifidobacterium polysaccharolyticum	strain=W8117	GCA_016101585.1	2750967	2750967	type	True	90.6383	563	688	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	78.2711	199	688	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	77.8288	150	688	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.1311	97	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:55,799] [INFO] DFAST Taxonomy check result was written to GCF_020884755.1_ASM2088475v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:55,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:55,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:55,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/checkm_data
[2024-01-24 13:17:55,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:55,825] [INFO] Task started: CheckM
[2024-01-24 13:17:55,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020884755.1_ASM2088475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020884755.1_ASM2088475v1_genomic.fna/checkm_input GCF_020884755.1_ASM2088475v1_genomic.fna/checkm_result
[2024-01-24 13:18:20,345] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:20,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,366] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:20,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:20,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020884755.1_ASM2088475v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:20,368] [INFO] Task started: Blastn
[2024-01-24 13:18:20,368] [INFO] Running command: blastn -query GCF_020884755.1_ASM2088475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac052ad-34f5-4716-96eb-cc949858f657/dqc_reference/reference_markers_gtdb.fasta -out GCF_020884755.1_ASM2088475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:21,622] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:21,628] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:21,628] [INFO] Target genome list was writen to GCF_020884755.1_ASM2088475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:21,720] [INFO] Task started: fastANI
[2024-01-24 13:18:21,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e52fe9-81c6-4c10-a66f-103e847faaba/GCF_020884755.1_ASM2088475v1_genomic.fna.gz --refList GCF_020884755.1_ASM2088475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020884755.1_ASM2088475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:27,061] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:27,083] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:27,083] [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_000499185.1	s__Bifidobacterium sp000499185	96.093	608	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	conclusive
GCF_000967185.1	s__Bifidobacterium asteroides_B	94.1343	618	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	91.883	565	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_016100725.1	s__Bifidobacterium sp016100725	91.7181	568	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	91.7154	555	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000499285.1	s__Bifidobacterium sp000499285	91.4606	571	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002715865.1	s__Bifidobacterium asteroides	91.138	575	688	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	90.9602	554	688	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	90.6284	570	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	-
GCF_003202695.1	s__Bifidobacterium asteroides_G	89.5465	538	688	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,085] [INFO] GTDB search result was written to GCF_020884755.1_ASM2088475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:27,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:27,091] [INFO] DFAST_QC result json was written to GCF_020884755.1_ASM2088475v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:27,092] [INFO] DFAST_QC completed!
[2024-01-24 13:18:27,092] [INFO] Total running time: 0h0m45s