[2024-01-24 12:14:07,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:07,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:07,141] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference
[2024-01-24 12:14:08,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:08,450] [INFO] Task started: Prodigal
[2024-01-24 12:14:08,450] [INFO] Running command: gunzip -c /var/lib/cwl/stge2930e56-da10-4111-b653-3182695ed4d7/GCF_010667615.1_ASM1066761v1_genomic.fna.gz | prodigal -d GCF_010667615.1_ASM1066761v1_genomic.fna/cds.fna -a GCF_010667615.1_ASM1066761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,026] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,026] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,026] [INFO] Running command: hmmsearch --tblout GCF_010667615.1_ASM1066761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/reference_markers.hmm GCF_010667615.1_ASM1066761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:15,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:15,255] [INFO] Found 6/6 markers.
[2024-01-24 12:14:15,277] [INFO] Query marker FASTA was written to GCF_010667615.1_ASM1066761v1_genomic.fna/markers.fasta
[2024-01-24 12:14:15,277] [INFO] Task started: Blastn
[2024-01-24 12:14:15,277] [INFO] Running command: blastn -query GCF_010667615.1_ASM1066761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/reference_markers.fasta -out GCF_010667615.1_ASM1066761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:16,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:16,491] [INFO] Selected 21 target genomes.
[2024-01-24 12:14:16,491] [INFO] Target genome list was writen to GCF_010667615.1_ASM1066761v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:16,504] [INFO] Task started: fastANI
[2024-01-24 12:14:16,504] [INFO] Running command: fastANI --query /var/lib/cwl/stge2930e56-da10-4111-b653-3182695ed4d7/GCF_010667615.1_ASM1066761v1_genomic.fna.gz --refList GCF_010667615.1_ASM1066761v1_genomic.fna/target_genomes.txt --output GCF_010667615.1_ASM1066761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:27,714] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:27,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:27,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:27,731] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:27,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:27,731] [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 choloepi	strain=BRDM 6	GCA_010667615.1	2614131	2614131	type	True	100.0	744	744	95	conclusive
Bifidobacterium choerinum	strain=DSM 20434	GCA_000771425.1	35760	35760	type	True	82.58	414	744	95	below_threshold
Bifidobacterium choerinum	strain=LMG 10510	GCA_000741135.1	35760	35760	type	True	82.5575	444	744	95	below_threshold
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	82.5431	431	744	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	82.5029	441	744	95	below_threshold
Bifidobacterium castoris	strain=2020B	GCA_003952025.1	2306972	2306972	type	True	82.4328	449	744	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	81.7416	390	744	95	below_threshold
Bifidobacterium ramosum	strain=DSM 100688	GCA_009299505.1	1798158	1798158	type	True	81.5336	373	744	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	81.4578	397	744	95	below_threshold
Bifidobacterium ramosum	strain=TREM	GCA_010667665.1	1798158	1798158	type	True	81.4363	377	744	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	81.4142	373	744	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.3959	373	744	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	81.2278	355	744	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	81.2267	377	744	95	below_threshold
Bifidobacterium cuniculi	strain=LMG 10738	GCA_000741575.1	1688	1688	type	True	80.9211	352	744	95	below_threshold
Bifidobacterium cuniculi	strain=DSM 20435	GCA_000771465.1	1688	1688	type	True	80.8669	329	744	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	80.7355	366	744	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.6542	335	744	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.5205	338	744	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.4858	187	744	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.2804	169	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,733] [INFO] DFAST Taxonomy check result was written to GCF_010667615.1_ASM1066761v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:27,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:27,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:27,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/checkm_data
[2024-01-24 12:14:27,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:27,761] [INFO] Task started: CheckM
[2024-01-24 12:14:27,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010667615.1_ASM1066761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010667615.1_ASM1066761v1_genomic.fna/checkm_input GCF_010667615.1_ASM1066761v1_genomic.fna/checkm_result
[2024-01-24 12:14:52,369] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:52,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:52,387] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:52,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:52,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010667615.1_ASM1066761v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:52,389] [INFO] Task started: Blastn
[2024-01-24 12:14:52,389] [INFO] Running command: blastn -query GCF_010667615.1_ASM1066761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab4c185-91c5-4812-b3fc-3a41e4e25e36/dqc_reference/reference_markers_gtdb.fasta -out GCF_010667615.1_ASM1066761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:54,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:54,302] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:54,302] [INFO] Target genome list was writen to GCF_010667615.1_ASM1066761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:54,316] [INFO] Task started: fastANI
[2024-01-24 12:14:54,317] [INFO] Running command: fastANI --query /var/lib/cwl/stge2930e56-da10-4111-b653-3182695ed4d7/GCF_010667615.1_ASM1066761v1_genomic.fna.gz --refList GCF_010667615.1_ASM1066761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010667615.1_ASM1066761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:02,820] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:02,838] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:02,838] [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_010667615.1	s__Bifidobacterium choloepi	100.0	744	744	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_000741135.1	s__Bifidobacterium choerinum	82.5935	442	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_002286915.1	s__Bifidobacterium italicum	82.5291	432	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952025.1	s__Bifidobacterium castoris	82.4652	446	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860345.1	s__Bifidobacterium anseris	82.3394	417	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.21	99.21	0.95	0.95	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	81.741	390	744	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	81.5225	373	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	81.4537	398	744	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	81.4152	373	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	81.2393	375	744	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	81.2036	357	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	81.0536	380	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_009299475.1	s__Bifidobacterium avesanii	81.0149	346	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741575.1	s__Bifidobacterium cuniculi	80.8929	354	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:02,840] [INFO] GTDB search result was written to GCF_010667615.1_ASM1066761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:02,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:02,844] [INFO] DFAST_QC result json was written to GCF_010667615.1_ASM1066761v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:02,844] [INFO] DFAST_QC completed!
[2024-01-24 12:15:02,844] [INFO] Total running time: 0h0m56s