[2023-06-13 23:45:17,537] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:45:17,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:45:17,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference
[2023-06-13 23:45:19,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:45:19,199] [INFO] Task started: Prodigal
[2023-06-13 23:45:19,200] [INFO] Running command: gunzip -c /var/lib/cwl/stge42f47d5-ef77-47a7-b5fa-1bd70a16b166/GCA_022649705.1_ASM2264970v1_genomic.fna.gz | prodigal -d GCA_022649705.1_ASM2264970v1_genomic.fna/cds.fna -a GCA_022649705.1_ASM2264970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:45:25,146] [INFO] Task succeeded: Prodigal
[2023-06-13 23:45:25,147] [INFO] Task started: HMMsearch
[2023-06-13 23:45:25,147] [INFO] Running command: hmmsearch --tblout GCA_022649705.1_ASM2264970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/reference_markers.hmm GCA_022649705.1_ASM2264970v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:45:25,339] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:45:25,343] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge42f47d5-ef77-47a7-b5fa-1bd70a16b166/GCA_022649705.1_ASM2264970v1_genomic.fna.gz]
[2023-06-13 23:45:25,361] [INFO] Query marker FASTA was written to GCA_022649705.1_ASM2264970v1_genomic.fna/markers.fasta
[2023-06-13 23:45:25,362] [INFO] Task started: Blastn
[2023-06-13 23:45:25,362] [INFO] Running command: blastn -query GCA_022649705.1_ASM2264970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/reference_markers.fasta -out GCA_022649705.1_ASM2264970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:45:26,053] [INFO] Task succeeded: Blastn
[2023-06-13 23:45:26,056] [INFO] Selected 18 target genomes.
[2023-06-13 23:45:26,057] [INFO] Target genome list was writen to GCA_022649705.1_ASM2264970v1_genomic.fna/target_genomes.txt
[2023-06-13 23:45:26,059] [INFO] Task started: fastANI
[2023-06-13 23:45:26,059] [INFO] Running command: fastANI --query /var/lib/cwl/stge42f47d5-ef77-47a7-b5fa-1bd70a16b166/GCA_022649705.1_ASM2264970v1_genomic.fna.gz --refList GCA_022649705.1_ASM2264970v1_genomic.fna/target_genomes.txt --output GCA_022649705.1_ASM2264970v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:45:34,387] [INFO] Task succeeded: fastANI
[2023-06-13 23:45:34,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:45:34,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:45:34,398] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 23:45:34,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 23:45:34,398] [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 crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	96.9352	600	668	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	81.0955	341	668	95	below_threshold
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	81.0857	334	668	95	below_threshold
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	80.9939	332	668	95	below_threshold
Bifidobacterium aquikefiri	strain=LMG 28769	GCA_002259795.1	1653207	1653207	type	True	78.4212	103	668	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	77.8592	122	668	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.7635	81	668	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.6823	118	668	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	77.5077	128	668	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	77.4786	120	668	95	below_threshold
Bifidobacterium felsineum	strain=TRE H	GCA_002802915.1	2045440	2045440	type	True	77.3405	108	668	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_000771125.1	1684	1684	suspected-type	True	76.8767	89	668	95	below_threshold
Bifidobacterium asteroides	strain=DSM 20089	GCA_002715865.1	1684	1684	suspected-type	True	76.8599	94	668	95	below_threshold
Bifidobacterium choladohabitans	strain=B14384H11	GCA_016102005.1	2750947	2750947	type	True	76.7925	91	668	95	below_threshold
Bifidobacterium polysaccharolyticum	strain=W8117	GCA_016101585.1	2750967	2750967	type	True	76.7346	101	668	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:45:34,400] [INFO] DFAST Taxonomy check result was written to GCA_022649705.1_ASM2264970v1_genomic.fna/tc_result.tsv
[2023-06-13 23:45:34,401] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:45:34,401] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:45:34,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/checkm_data
[2023-06-13 23:45:34,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:45:34,426] [INFO] Task started: CheckM
[2023-06-13 23:45:34,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022649705.1_ASM2264970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022649705.1_ASM2264970v1_genomic.fna/checkm_input GCA_022649705.1_ASM2264970v1_genomic.fna/checkm_result
[2023-06-13 23:45:56,612] [INFO] Task succeeded: CheckM
[2023-06-13 23:45:56,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:45:56,628] [INFO] ===== Completeness check finished =====
[2023-06-13 23:45:56,629] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:45:56,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022649705.1_ASM2264970v1_genomic.fna/markers.fasta)
[2023-06-13 23:45:56,629] [INFO] Task started: Blastn
[2023-06-13 23:45:56,629] [INFO] Running command: blastn -query GCA_022649705.1_ASM2264970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd66bd309-c521-42dc-a69c-88f8c1cc2414/dqc_reference/reference_markers_gtdb.fasta -out GCA_022649705.1_ASM2264970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:45:57,593] [INFO] Task succeeded: Blastn
[2023-06-13 23:45:57,596] [INFO] Selected 18 target genomes.
[2023-06-13 23:45:57,596] [INFO] Target genome list was writen to GCA_022649705.1_ASM2264970v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:45:57,601] [INFO] Task started: fastANI
[2023-06-13 23:45:57,601] [INFO] Running command: fastANI --query /var/lib/cwl/stge42f47d5-ef77-47a7-b5fa-1bd70a16b166/GCA_022649705.1_ASM2264970v1_genomic.fna.gz --refList GCA_022649705.1_ASM2264970v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022649705.1_ASM2264970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:46:05,198] [INFO] Task succeeded: fastANI
[2023-06-13 23:46:05,209] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 23:46:05,210] [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_000738005.1	s__Bifidobacterium crudilactis	96.9352	600	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	conclusive
GCF_000741705.1	s__Bifidobacterium psychraerophilum	81.0857	334	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	78.4212	103	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741285.1	s__Bifidobacterium mongoliense	78.2744	138	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_002802905.1	s__Galliscardovia simiarum	77.8573	122	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_003952005.1	s__Galliscardovia callimiconis	77.8558	106	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_002860355.1	s__Galliscardovia margollesii	77.7828	111	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259645.1	s__Galliscardovia tissieri	77.6187	109	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	77.6091	129	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000741775.1	s__Bifidobacterium subtile	77.5602	129	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_001042635.1	s__Bifidobacterium scardovii	77.5238	130	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_014898155.1	s__Bifidobacterium eulemuris	77.5077	128	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002802915.1	s__Bifidobacterium felsineum	77.3405	108	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_002715865.1	s__Bifidobacterium asteroides	76.8599	94	668	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	76.8374	93	668	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	76.8358	96	668	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	76.7867	96	668	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	76.776	101	668	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:46:05,213] [INFO] GTDB search result was written to GCA_022649705.1_ASM2264970v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:46:05,213] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:46:05,217] [INFO] DFAST_QC result json was written to GCA_022649705.1_ASM2264970v1_genomic.fna/dqc_result.json
[2023-06-13 23:46:05,217] [INFO] DFAST_QC completed!
[2023-06-13 23:46:05,217] [INFO] Total running time: 0h0m48s