[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference
[2024-01-24 11:12:38,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,664] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c28c57d-a81b-4634-8213-9468254de679/GCF_002860365.1_ASM286036v1_genomic.fna.gz | prodigal -d GCF_002860365.1_ASM286036v1_genomic.fna/cds.fna -a GCF_002860365.1_ASM286036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,081] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,082] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,082] [INFO] Running command: hmmsearch --tblout GCF_002860365.1_ASM286036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/reference_markers.hmm GCF_002860365.1_ASM286036v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,257] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,258] [INFO] Found 6/6 markers.
[2024-01-24 11:12:47,299] [INFO] Query marker FASTA was written to GCF_002860365.1_ASM286036v1_genomic.fna/markers.fasta
[2024-01-24 11:12:47,300] [INFO] Task started: Blastn
[2024-01-24 11:12:47,300] [INFO] Running command: blastn -query GCF_002860365.1_ASM286036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/reference_markers.fasta -out GCF_002860365.1_ASM286036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,366] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,369] [INFO] Selected 14 target genomes.
[2024-01-24 11:12:48,369] [INFO] Target genome list was writen to GCF_002860365.1_ASM286036v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,412] [INFO] Task started: fastANI
[2024-01-24 11:12:48,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c28c57d-a81b-4634-8213-9468254de679/GCF_002860365.1_ASM286036v1_genomic.fna.gz --refList GCF_002860365.1_ASM286036v1_genomic.fna/target_genomes.txt --output GCF_002860365.1_ASM286036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:56,633] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:56,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:56,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:56,646] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:56,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:56,646] [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 parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	100.0	919	919	95	conclusive
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	94.1863	715	919	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	90.6443	631	919	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	88.2301	629	919	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	87.4672	589	919	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	87.3465	598	919	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	86.6747	577	919	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000771665.1	762209	762209	type	True	86.6688	571	919	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	86.6434	583	919	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	84.48	502	919	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.7567	527	919	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.0838	315	919	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.3749	157	919	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	76.8869	110	919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:56,648] [INFO] DFAST Taxonomy check result was written to GCF_002860365.1_ASM286036v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:56,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:56,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:56,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/checkm_data
[2024-01-24 11:12:56,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:56,677] [INFO] Task started: CheckM
[2024-01-24 11:12:56,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002860365.1_ASM286036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002860365.1_ASM286036v1_genomic.fna/checkm_input GCF_002860365.1_ASM286036v1_genomic.fna/checkm_result
[2024-01-24 11:13:26,314] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:26,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:26,331] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:26,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:26,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002860365.1_ASM286036v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:26,332] [INFO] Task started: Blastn
[2024-01-24 11:13:26,332] [INFO] Running command: blastn -query GCF_002860365.1_ASM286036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac3ab00-2ace-4e53-8787-a41eda31da74/dqc_reference/reference_markers_gtdb.fasta -out GCF_002860365.1_ASM286036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:27,963] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:27,966] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:27,966] [INFO] Target genome list was writen to GCF_002860365.1_ASM286036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:27,974] [INFO] Task started: fastANI
[2024-01-24 11:13:27,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c28c57d-a81b-4634-8213-9468254de679/GCF_002860365.1_ASM286036v1_genomic.fna.gz --refList GCF_002860365.1_ASM286036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002860365.1_ASM286036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:33,973] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:33,981] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:33,981] [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_002860365.1	s__Bifidobacterium parmae	100.0	919	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000741785.1	s__Bifidobacterium stellenboschense	94.1831	716	919	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	90.6184	632	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	88.2345	629	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	87.456	590	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	87.3738	620	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741175.1	s__Bifidobacterium callitrichos	86.7227	574	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_008698235.1	s__Bifidobacterium rousetti	86.651	583	919	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	84.2251	496	919	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 11:13:33,982] [INFO] GTDB search result was written to GCF_002860365.1_ASM286036v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:33,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:33,986] [INFO] DFAST_QC result json was written to GCF_002860365.1_ASM286036v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:33,986] [INFO] DFAST_QC completed!
[2024-01-24 11:13:33,987] [INFO] Total running time: 0h0m58s