[2024-01-24 13:32:18,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,867] [INFO] DQC Reference Directory: /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference
[2024-01-24 13:32:20,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:20,176] [INFO] Task started: Prodigal
[2024-01-24 13:32:20,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg41cb338f-b1d5-4b0d-91a2-4d0ee1e732ff/GCF_003315635.1_ASM331563v1_genomic.fna.gz | prodigal -d GCF_003315635.1_ASM331563v1_genomic.fna/cds.fna -a GCF_003315635.1_ASM331563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:26,877] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:26,878] [INFO] Task started: HMMsearch
[2024-01-24 13:32:26,878] [INFO] Running command: hmmsearch --tblout GCF_003315635.1_ASM331563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/reference_markers.hmm GCF_003315635.1_ASM331563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:27,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:27,127] [INFO] Found 6/6 markers.
[2024-01-24 13:32:27,150] [INFO] Query marker FASTA was written to GCF_003315635.1_ASM331563v1_genomic.fna/markers.fasta
[2024-01-24 13:32:27,150] [INFO] Task started: Blastn
[2024-01-24 13:32:27,150] [INFO] Running command: blastn -query GCF_003315635.1_ASM331563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/reference_markers.fasta -out GCF_003315635.1_ASM331563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:28,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:28,037] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:28,037] [INFO] Target genome list was writen to GCF_003315635.1_ASM331563v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:28,050] [INFO] Task started: fastANI
[2024-01-24 13:32:28,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cb338f-b1d5-4b0d-91a2-4d0ee1e732ff/GCF_003315635.1_ASM331563v1_genomic.fna.gz --refList GCF_003315635.1_ASM331563v1_genomic.fna/target_genomes.txt --output GCF_003315635.1_ASM331563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:38,926] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:38,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:38,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:38,945] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:38,945] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:38,945] [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 aemilianum	strain=XV10	GCA_003315635.1	2493120	2493120	type	True	100.0	648	651	95	conclusive
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	79.3803	213	651	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	79.2314	209	651	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	79.2032	233	651	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	79.1749	228	651	95	below_threshold
Bifidobacterium apousia	strain=W8102	GCA_007559275.1	2750996	2750996	type	True	79.1641	230	651	95	below_threshold
Bifidobacterium polysaccharolyticum	strain=W8117	GCA_016101585.1	2750967	2750967	type	True	79.0669	210	651	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	78.9957	194	651	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	78.7882	192	651	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	78.748	186	651	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	78.6963	198	651	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_014898175.1	1603886	1603886	type	True	78.5875	194	651	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	78.5857	181	651	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	78.5794	180	651	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	78.5191	190	651	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	78.5005	195	651	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	78.4949	181	651	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	78.4905	186	651	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	78.4354	195	651	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	78.4161	183	651	95	below_threshold
Bifidobacterium tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	78.2809	191	651	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	78.2758	169	651	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.2078	119	651	95	below_threshold
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	77.6873	149	651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,947] [INFO] DFAST Taxonomy check result was written to GCF_003315635.1_ASM331563v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:38,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:38,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:38,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/checkm_data
[2024-01-24 13:32:38,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:38,971] [INFO] Task started: CheckM
[2024-01-24 13:32:38,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315635.1_ASM331563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315635.1_ASM331563v1_genomic.fna/checkm_input GCF_003315635.1_ASM331563v1_genomic.fna/checkm_result
[2024-01-24 13:33:05,440] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:05,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:05,457] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:05,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:05,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315635.1_ASM331563v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:05,458] [INFO] Task started: Blastn
[2024-01-24 13:33:05,458] [INFO] Running command: blastn -query GCF_003315635.1_ASM331563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1d01be5-c94e-4f35-8a9c-c2dc6e3f8b78/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315635.1_ASM331563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:06,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:06,713] [INFO] Selected 24 target genomes.
[2024-01-24 13:33:06,713] [INFO] Target genome list was writen to GCF_003315635.1_ASM331563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:06,733] [INFO] Task started: fastANI
[2024-01-24 13:33:06,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg41cb338f-b1d5-4b0d-91a2-4d0ee1e732ff/GCF_003315635.1_ASM331563v1_genomic.fna.gz --refList GCF_003315635.1_ASM331563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315635.1_ASM331563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:17,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,178] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:17,178] [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_003315635.1	s__Bifidobacterium aemilianum	100.0	648	651	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_000967185.1	s__Bifidobacterium asteroides_B	79.5754	219	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.60	95.51	0.88	0.86	7	-
GCF_016100725.1	s__Bifidobacterium sp016100725	79.4097	230	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.87	96.39	0.95	0.91	9	-
GCF_002715865.1	s__Bifidobacterium asteroides	79.3897	213	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.35	97.73	0.95	0.92	9	-
GCF_000499185.1	s__Bifidobacterium sp000499185	79.3266	213	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.45	96.45	0.89	0.89	2	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	79.165	215	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	79.1642	210	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698145.1	s__Bifidobacterium vespertilionis	79.148	178	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	79.146	234	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_000499285.1	s__Bifidobacterium sp000499285	79.0986	217	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	79.0844	184	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.0271	194	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003202715.1	s__Bifidobacterium asteroides_E	78.9531	206	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.91	96.34	0.93	0.92	10	-
GCF_018555355.1	s__Bifidobacterium sp018555355	78.8941	225	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_012932365.1	s__Bifidobacterium sp012932365	78.7441	183	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741575.1	s__Bifidobacterium cuniculi	78.7018	185	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014898155.1	s__Bifidobacterium eulemuris	78.6553	197	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014898175.1	s__Bifidobacterium lemurum	78.6312	196	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003952945.1	s__Bifidobacterium samirii	78.6309	170	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	78.5857	181	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	78.5567	181	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_000741775.1	s__Bifidobacterium subtile	78.5165	180	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_001417815.1	s__Bifidobacterium aesculapii	78.2758	169	651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	77.6873	149	651	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 13:33:17,180] [INFO] GTDB search result was written to GCF_003315635.1_ASM331563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:17,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:17,185] [INFO] DFAST_QC result json was written to GCF_003315635.1_ASM331563v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:17,185] [INFO] DFAST_QC completed!
[2024-01-24 13:33:17,185] [INFO] Total running time: 0h0m58s