[2024-01-24 14:05:52,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:52,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:52,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference
[2024-01-24 14:05:54,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:54,325] [INFO] Task started: Prodigal
[2024-01-24 14:05:54,325] [INFO] Running command: gunzip -c /var/lib/cwl/stga3e9ca8d-02d3-4c01-a8b6-065b061af5be/GCF_002259755.1_ASM225975v1_genomic.fna.gz | prodigal -d GCF_002259755.1_ASM225975v1_genomic.fna/cds.fna -a GCF_002259755.1_ASM225975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:03,424] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:03,425] [INFO] Task started: HMMsearch
[2024-01-24 14:06:03,425] [INFO] Running command: hmmsearch --tblout GCF_002259755.1_ASM225975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/reference_markers.hmm GCF_002259755.1_ASM225975v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,720] [INFO] Found 6/6 markers.
[2024-01-24 14:06:03,766] [INFO] Query marker FASTA was written to GCF_002259755.1_ASM225975v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,766] [INFO] Task started: Blastn
[2024-01-24 14:06:03,766] [INFO] Running command: blastn -query GCF_002259755.1_ASM225975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/reference_markers.fasta -out GCF_002259755.1_ASM225975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:04,536] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:04,541] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:04,541] [INFO] Target genome list was writen to GCF_002259755.1_ASM225975v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:04,554] [INFO] Task started: fastANI
[2024-01-24 14:06:04,554] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e9ca8d-02d3-4c01-a8b6-065b061af5be/GCF_002259755.1_ASM225975v1_genomic.fna.gz --refList GCF_002259755.1_ASM225975v1_genomic.fna/target_genomes.txt --output GCF_002259755.1_ASM225975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:16,999] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:17,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:17,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:17,015] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:17,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:17,015] [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 hapali	strain=DSM 100202	GCA_002259755.1	1630172	1630172	type	True	100.0	906	907	95	conclusive
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	81.4606	412	907	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	81.2419	404	907	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	81.2379	420	907	95	below_threshold
Bifidobacterium miconis	strain=82T10	GCA_019331735.1	2834435	2834435	type	True	81.203	372	907	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	81.1898	419	907	95	below_threshold
Bifidobacterium goeldii	strain=2034B	GCA_003951095.1	2306975	2306975	type	True	80.9319	296	907	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	80.84	374	907	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000771645.1	762212	762212	type	True	80.7797	369	907	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.5076	371	907	95	below_threshold
Bifidobacterium catenulatum	strain=JCM 1194	GCA_001025195.1	1686	1686	type	True	79.2642	172	907	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	79.0706	166	907	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	78.8008	171	907	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	78.6661	173	907	95	below_threshold
Bifidobacterium boum	strain=LMG 10736	GCA_000741535.1	78343	78343	type	True	78.4868	151	907	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	78.4627	153	907	95	below_threshold
Bifidobacterium bohemicum	strain=DSM 22767	GCA_000741525.1	638617	638617	type	True	77.6945	89	907	95	below_threshold
Bifidobacterium bohemicum	strain=DSM 22767	GCA_000771605.1	638617	638617	type	True	77.4571	87	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,017] [INFO] DFAST Taxonomy check result was written to GCF_002259755.1_ASM225975v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:17,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:17,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:17,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/checkm_data
[2024-01-24 14:06:17,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:17,060] [INFO] Task started: CheckM
[2024-01-24 14:06:17,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259755.1_ASM225975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259755.1_ASM225975v1_genomic.fna/checkm_input GCF_002259755.1_ASM225975v1_genomic.fna/checkm_result
[2024-01-24 14:06:49,531] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:49,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,552] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:49,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:49,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259755.1_ASM225975v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:49,553] [INFO] Task started: Blastn
[2024-01-24 14:06:49,553] [INFO] Running command: blastn -query GCF_002259755.1_ASM225975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36790a2d-aa4b-418d-97a8-f838f7603a46/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259755.1_ASM225975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,520] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,523] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:50,523] [INFO] Target genome list was writen to GCF_002259755.1_ASM225975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:50,539] [INFO] Task started: fastANI
[2024-01-24 14:06:50,539] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e9ca8d-02d3-4c01-a8b6-065b061af5be/GCF_002259755.1_ASM225975v1_genomic.fna.gz --refList GCF_002259755.1_ASM225975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259755.1_ASM225975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:59,610] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,624] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:59,624] [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_002259755.1	s__Bifidobacterium hapali	100.0	906	907	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_018555335.1	s__Bifidobacterium sp018555335	81.6917	430	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	81.2149	406	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299505.1	s__Bifidobacterium ramosum	81.1898	419	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003951095.1	s__Bifidobacterium goeldii	80.9319	296	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	80.8572	373	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000741175.1	s__Bifidobacterium callitrichos	80.8389	259	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_012932375.1	s__Bifidobacterium sp012932375	80.4353	225	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	79.4302	226	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001025195.1	s__Bifidobacterium catenulatum	79.3067	170	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.2025	193	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	79.1959	178	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_012932425.1	s__Bifidobacterium sp012932425	78.956	198	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770925.1	s__Bifidobacterium ruminantium	78.8008	171	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_001042595.1	s__Bifidobacterium dentium	78.7731	199	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_000741535.1	s__Bifidobacterium boum	78.4868	151	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	-
GCF_000741525.1	s__Bifidobacterium bohemicum	77.6945	89	907	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,626] [INFO] GTDB search result was written to GCF_002259755.1_ASM225975v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:59,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:59,631] [INFO] DFAST_QC result json was written to GCF_002259755.1_ASM225975v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:59,631] [INFO] DFAST_QC completed!
[2024-01-24 14:06:59,631] [INFO] Total running time: 0h1m7s