[2024-01-24 11:26:54,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference
[2024-01-24 11:26:58,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg27bf7f5a-dd7d-4704-a08d-c70f46f4df4c/GCF_000741285.1_Bifmon_genomic.fna.gz | prodigal -d GCF_000741285.1_Bifmon_genomic.fna/cds.fna -a GCF_000741285.1_Bifmon_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:05,443] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:05,444] [INFO] Task started: HMMsearch
[2024-01-24 11:27:05,444] [INFO] Running command: hmmsearch --tblout GCF_000741285.1_Bifmon_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/reference_markers.hmm GCF_000741285.1_Bifmon_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:05,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:05,693] [INFO] Found 6/6 markers.
[2024-01-24 11:27:05,719] [INFO] Query marker FASTA was written to GCF_000741285.1_Bifmon_genomic.fna/markers.fasta
[2024-01-24 11:27:05,720] [INFO] Task started: Blastn
[2024-01-24 11:27:05,720] [INFO] Running command: blastn -query GCF_000741285.1_Bifmon_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/reference_markers.fasta -out GCF_000741285.1_Bifmon_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:06,640] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:06,644] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:06,645] [INFO] Target genome list was writen to GCF_000741285.1_Bifmon_genomic.fna/target_genomes.txt
[2024-01-24 11:27:06,654] [INFO] Task started: fastANI
[2024-01-24 11:27:06,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bf7f5a-dd7d-4704-a08d-c70f46f4df4c/GCF_000741285.1_Bifmon_genomic.fna.gz --refList GCF_000741285.1_Bifmon_genomic.fna/target_genomes.txt --output GCF_000741285.1_Bifmon_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:15,514] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:15,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:15,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:15,535] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:15,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:15,535] [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 mongoliense	strain=DSM 21395	GCA_000741285.1	518643	518643	type	True	99.9999	700	702	95	conclusive
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000771525.1	518643	518643	type	True	99.9536	680	702	95	conclusive
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.8509	259	702	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	79.8427	260	702	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	79.8065	307	702	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	79.7738	272	702	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	79.7732	282	702	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	79.7705	269	702	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	79.7225	290	702	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	79.7134	297	702	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	79.5271	251	702	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	79.4959	254	702	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.4446	263	702	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_001895165.1	1603886	1603886	type	True	79.3878	246	702	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	79.3296	246	702	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	78.9716	273	702	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.4098	191	702	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.8973	153	702	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.7593	60	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:15,544] [INFO] DFAST Taxonomy check result was written to GCF_000741285.1_Bifmon_genomic.fna/tc_result.tsv
[2024-01-24 11:27:15,545] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:15,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:15,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/checkm_data
[2024-01-24 11:27:15,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:15,575] [INFO] Task started: CheckM
[2024-01-24 11:27:15,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741285.1_Bifmon_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741285.1_Bifmon_genomic.fna/checkm_input GCF_000741285.1_Bifmon_genomic.fna/checkm_result
[2024-01-24 11:27:42,917] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:42,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:42,938] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:42,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:42,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741285.1_Bifmon_genomic.fna/markers.fasta)
[2024-01-24 11:27:42,939] [INFO] Task started: Blastn
[2024-01-24 11:27:42,939] [INFO] Running command: blastn -query GCF_000741285.1_Bifmon_genomic.fna/markers.fasta -db /var/lib/cwl/stg01bcf0da-f999-4e1f-9fa6-78e56a137c20/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741285.1_Bifmon_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:44,454] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:44,459] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:44,459] [INFO] Target genome list was writen to GCF_000741285.1_Bifmon_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:44,474] [INFO] Task started: fastANI
[2024-01-24 11:27:44,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bf7f5a-dd7d-4704-a08d-c70f46f4df4c/GCF_000741285.1_Bifmon_genomic.fna.gz --refList GCF_000741285.1_Bifmon_genomic.fna/target_genomes_gtdb.txt --output GCF_000741285.1_Bifmon_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:53,660] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:53,677] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:53,677] [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_000741285.1	s__Bifidobacterium mongoliense	99.9999	700	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	conclusive
GCF_018555385.1	s__Bifidobacterium sp018555385	79.8229	261	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741775.1	s__Bifidobacterium subtile	79.816	306	702	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	79.7758	274	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_012932365.1	s__Bifidobacterium sp012932365	79.6814	254	702	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	79.6576	268	702	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	79.634	269	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016899725.1	s__Bifidobacterium pullorum_C	79.6095	261	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.5738	248	702	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	79.535	252	702	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	79.5271	251	702	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	79.5021	253	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.4789	242	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003952945.1	s__Bifidobacterium samirii	79.4709	255	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	79.4513	246	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_014898155.1	s__Bifidobacterium eulemuris	79.3427	252	702	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	79.3072	254	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001025135.1	s__Bifidobacterium bifidum	79.2112	240	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	-
GCF_009299505.1	s__Bifidobacterium ramosum	79.1808	265	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741165.1	s__Bifidobacterium biavatii	79.0115	252	702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,679] [INFO] GTDB search result was written to GCF_000741285.1_Bifmon_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:53,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:53,684] [INFO] DFAST_QC result json was written to GCF_000741285.1_Bifmon_genomic.fna/dqc_result.json
[2024-01-24 11:27:53,684] [INFO] DFAST_QC completed!
[2024-01-24 11:27:53,684] [INFO] Total running time: 0h0m59s