[2024-01-24 11:26:54,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference
[2024-01-24 11:26:58,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,222] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c102e9d-06f7-42c5-a313-826df2a3aca5/GCF_002813205.1_ASM281320v1_genomic.fna.gz | prodigal -d GCF_002813205.1_ASM281320v1_genomic.fna/cds.fna -a GCF_002813205.1_ASM281320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:07,171] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:07,172] [INFO] Task started: HMMsearch
[2024-01-24 11:27:07,172] [INFO] Running command: hmmsearch --tblout GCF_002813205.1_ASM281320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/reference_markers.hmm GCF_002813205.1_ASM281320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:07,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:07,415] [INFO] Found 6/6 markers.
[2024-01-24 11:27:07,437] [INFO] Query marker FASTA was written to GCF_002813205.1_ASM281320v1_genomic.fna/markers.fasta
[2024-01-24 11:27:07,437] [INFO] Task started: Blastn
[2024-01-24 11:27:07,437] [INFO] Running command: blastn -query GCF_002813205.1_ASM281320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/reference_markers.fasta -out GCF_002813205.1_ASM281320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:08,103] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:08,107] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:08,107] [INFO] Target genome list was writen to GCF_002813205.1_ASM281320v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:08,155] [INFO] Task started: fastANI
[2024-01-24 11:27:08,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c102e9d-06f7-42c5-a313-826df2a3aca5/GCF_002813205.1_ASM281320v1_genomic.fna.gz --refList GCF_002813205.1_ASM281320v1_genomic.fna/target_genomes.txt --output GCF_002813205.1_ASM281320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:17,113] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:17,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:17,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:17,131] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:27:17,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:17,132] [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 psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	100.0	876	877	95	conclusive
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	99.9821	864	877	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	99.9593	842	877	95	conclusive
Bifidobacterium crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	81.0474	387	877	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	77.7586	162	877	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	77.7089	158	877	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	77.6769	151	877	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	77.6199	144	877	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	77.575	174	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,134] [INFO] DFAST Taxonomy check result was written to GCF_002813205.1_ASM281320v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:17,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:17,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:17,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/checkm_data
[2024-01-24 11:27:17,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:17,163] [INFO] Task started: CheckM
[2024-01-24 11:27:17,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813205.1_ASM281320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813205.1_ASM281320v1_genomic.fna/checkm_input GCF_002813205.1_ASM281320v1_genomic.fna/checkm_result
[2024-01-24 11:27:49,824] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:49,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,843] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:49,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:49,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813205.1_ASM281320v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:49,844] [INFO] Task started: Blastn
[2024-01-24 11:27:49,844] [INFO] Running command: blastn -query GCF_002813205.1_ASM281320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg994042b0-2317-4192-837d-8ecc2d19de03/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813205.1_ASM281320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:50,727] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:50,731] [INFO] Selected 23 target genomes.
[2024-01-24 11:27:50,731] [INFO] Target genome list was writen to GCF_002813205.1_ASM281320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:50,751] [INFO] Task started: fastANI
[2024-01-24 11:27:50,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c102e9d-06f7-42c5-a313-826df2a3aca5/GCF_002813205.1_ASM281320v1_genomic.fna.gz --refList GCF_002813205.1_ASM281320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813205.1_ASM281320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:02,490] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:02,508] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:02,508] [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_000741705.1	s__Bifidobacterium psychraerophilum	99.9821	864	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_000738005.1	s__Bifidobacterium crudilactis	81.0474	387	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	-
GCF_000741775.1	s__Bifidobacterium subtile	78.941	169	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	78.7967	136	877	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	78.515	156	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_001042635.1	s__Bifidobacterium scardovii	78.0244	164	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555635.1	s__Bifidobacterium sp018555635	78.0163	131	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	77.9387	142	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014898155.1	s__Bifidobacterium eulemuris	77.821	178	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.7578	140	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001042595.1	s__Bifidobacterium dentium	77.6989	150	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_014898175.1	s__Bifidobacterium lemurum	77.6908	177	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.6229	137	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	77.6199	144	877	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	77.5868	118	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	77.5742	164	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_012932675.1	s__Bifidobacterium sp012932675	77.4105	149	877	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	77.3899	142	877	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667615.1	s__Bifidobacterium choloepi	77.3758	112	877	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 11:28:02,510] [INFO] GTDB search result was written to GCF_002813205.1_ASM281320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:02,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:02,514] [INFO] DFAST_QC result json was written to GCF_002813205.1_ASM281320v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:02,514] [INFO] DFAST_QC completed!
[2024-01-24 11:28:02,514] [INFO] Total running time: 0h1m8s