[2024-01-24 12:06:19,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:19,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:19,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference
[2024-01-24 12:06:20,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,359] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbf2abe-b8f4-4dbe-9edb-562a2f41ab65/GCF_000741365.1_Bifrum_genomic.fna.gz | prodigal -d GCF_000741365.1_Bifrum_genomic.fna/cds.fna -a GCF_000741365.1_Bifrum_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,942] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,942] [INFO] Running command: hmmsearch --tblout GCF_000741365.1_Bifrum_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/reference_markers.hmm GCF_000741365.1_Bifrum_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,161] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,183] [INFO] Query marker FASTA was written to GCF_000741365.1_Bifrum_genomic.fna/markers.fasta
[2024-01-24 12:06:28,184] [INFO] Task started: Blastn
[2024-01-24 12:06:28,184] [INFO] Running command: blastn -query GCF_000741365.1_Bifrum_genomic.fna/markers.fasta -db /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/reference_markers.fasta -out GCF_000741365.1_Bifrum_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,057] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,062] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:29,062] [INFO] Target genome list was writen to GCF_000741365.1_Bifrum_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,066] [INFO] Task started: fastANI
[2024-01-24 12:06:29,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf2abe-b8f4-4dbe-9edb-562a2f41ab65/GCF_000741365.1_Bifrum_genomic.fna.gz --refList GCF_000741365.1_Bifrum_genomic.fna/target_genomes.txt --output GCF_000741365.1_Bifrum_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,614] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,626] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:35,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,627] [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 ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	99.9514	707	739	95	conclusive
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	99.9429	709	739	95	conclusive
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	88.6637	525	739	95	below_threshold
Bifidobacterium adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	88.6203	532	739	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	83.4579	414	739	95	below_threshold
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	83.2663	457	739	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	83.0421	439	739	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	82.937	460	739	95	below_threshold
Bifidobacterium dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	82.7597	445	739	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.2161	360	739	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.2617	253	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,628] [INFO] DFAST Taxonomy check result was written to GCF_000741365.1_Bifrum_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,629] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/checkm_data
[2024-01-24 12:06:35,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,665] [INFO] Task started: CheckM
[2024-01-24 12:06:35,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741365.1_Bifrum_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741365.1_Bifrum_genomic.fna/checkm_input GCF_000741365.1_Bifrum_genomic.fna/checkm_result
[2024-01-24 12:07:03,496] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:03,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:03,523] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:03,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:03,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741365.1_Bifrum_genomic.fna/markers.fasta)
[2024-01-24 12:07:03,524] [INFO] Task started: Blastn
[2024-01-24 12:07:03,525] [INFO] Running command: blastn -query GCF_000741365.1_Bifrum_genomic.fna/markers.fasta -db /var/lib/cwl/stg99384a6d-d1b3-4c8a-8cb2-241533a310b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741365.1_Bifrum_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:04,728] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:04,732] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:04,732] [INFO] Target genome list was writen to GCF_000741365.1_Bifrum_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:04,739] [INFO] Task started: fastANI
[2024-01-24 12:07:04,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf2abe-b8f4-4dbe-9edb-562a2f41ab65/GCF_000741365.1_Bifrum_genomic.fna.gz --refList GCF_000741365.1_Bifrum_genomic.fna/target_genomes_gtdb.txt --output GCF_000741365.1_Bifrum_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:10,257] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,274] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:10,274] [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_000770925.1	s__Bifidobacterium ruminantium	99.9514	707	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	conclusive
GCF_000010425.1	s__Bifidobacterium adolescentis	88.63	531	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCA_002451435.1	s__Bifidobacterium sp002451435	83.93	408	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_001025195.1	s__Bifidobacterium catenulatum	83.394	450	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_000522505.1	s__Bifidobacterium moukalabense	83.2761	458	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	83.1404	467	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	83.1363	455	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	82.9846	449	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_002742445.1	s__Bifidobacterium sp002742445	82.9758	440	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001042595.1	s__Bifidobacterium dentium	82.7416	446	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_018555355.1	s__Bifidobacterium sp018555355	81.5191	353	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,276] [INFO] GTDB search result was written to GCF_000741365.1_Bifrum_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:10,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:10,280] [INFO] DFAST_QC result json was written to GCF_000741365.1_Bifrum_genomic.fna/dqc_result.json
[2024-01-24 12:07:10,280] [INFO] DFAST_QC completed!
[2024-01-24 12:07:10,281] [INFO] Total running time: 0h0m51s