[2024-01-25 17:43:50,692] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference
[2024-01-25 17:43:51,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,813] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d6f578e-407a-4263-9e37-86feea5b401c/GCF_000771085.1_DSM-19703_genomic.fna.gz | prodigal -d GCF_000771085.1_DSM-19703_genomic.fna/cds.fna -a GCF_000771085.1_DSM-19703_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:57,353] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:57,353] [INFO] Task started: HMMsearch
[2024-01-25 17:43:57,353] [INFO] Running command: hmmsearch --tblout GCF_000771085.1_DSM-19703_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/reference_markers.hmm GCF_000771085.1_DSM-19703_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:57,529] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:57,530] [INFO] Found 6/6 markers.
[2024-01-25 17:43:57,548] [INFO] Query marker FASTA was written to GCF_000771085.1_DSM-19703_genomic.fna/markers.fasta
[2024-01-25 17:43:57,548] [INFO] Task started: Blastn
[2024-01-25 17:43:57,548] [INFO] Running command: blastn -query GCF_000771085.1_DSM-19703_genomic.fna/markers.fasta -db /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/reference_markers.fasta -out GCF_000771085.1_DSM-19703_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:58,130] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:58,133] [INFO] Selected 25 target genomes.
[2024-01-25 17:43:58,134] [INFO] Target genome list was writen to GCF_000771085.1_DSM-19703_genomic.fna/target_genomes.txt
[2024-01-25 17:43:58,154] [INFO] Task started: fastANI
[2024-01-25 17:43:58,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d6f578e-407a-4263-9e37-86feea5b401c/GCF_000771085.1_DSM-19703_genomic.fna.gz --refList GCF_000771085.1_DSM-19703_genomic.fna/target_genomes.txt --output GCF_000771085.1_DSM-19703_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:08,121] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:08,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:08,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:08,135] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:44:08,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:08,135] [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 bombi	strain=DSM 19703	GCA_000771085.1	471511	471511	type	True	100.0	614	615	95	conclusive
Bifidobacterium bombi	strain=DSM 19703	GCA_000737845.1	471511	471511	type	True	99.9685	612	615	95	conclusive
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	77.8606	83	615	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	77.6186	72	615	95	below_threshold
Bifidobacterium subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	77.6014	103	615	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000771005.1	79262	246618	type	True	77.5992	76	615	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	77.5817	103	615	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	77.5241	104	615	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	77.5087	92	615	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.4764	86	615	95	below_threshold
Bifidobacterium adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	77.4746	80	615	95	below_threshold
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	77.4598	81	615	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	77.4265	92	615	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	77.4234	97	615	95	below_threshold
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	77.3555	87	615	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	77.3506	101	615	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	77.3427	97	615	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	77.3376	73	615	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	77.3085	88	615	95	below_threshold
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	77.2947	82	615	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	77.2485	82	615	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	77.1007	91	615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:08,137] [INFO] DFAST Taxonomy check result was written to GCF_000771085.1_DSM-19703_genomic.fna/tc_result.tsv
[2024-01-25 17:44:08,138] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:08,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:08,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/checkm_data
[2024-01-25 17:44:08,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:08,164] [INFO] Task started: CheckM
[2024-01-25 17:44:08,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771085.1_DSM-19703_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771085.1_DSM-19703_genomic.fna/checkm_input GCF_000771085.1_DSM-19703_genomic.fna/checkm_result
[2024-01-25 17:44:29,251] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:29,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:29,267] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:29,267] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:29,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771085.1_DSM-19703_genomic.fna/markers.fasta)
[2024-01-25 17:44:29,267] [INFO] Task started: Blastn
[2024-01-25 17:44:29,267] [INFO] Running command: blastn -query GCF_000771085.1_DSM-19703_genomic.fna/markers.fasta -db /var/lib/cwl/stgf422eadc-f9ea-4710-8602-c7a141a246f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771085.1_DSM-19703_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:30,186] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:30,189] [INFO] Selected 26 target genomes.
[2024-01-25 17:44:30,189] [INFO] Target genome list was writen to GCF_000771085.1_DSM-19703_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:30,206] [INFO] Task started: fastANI
[2024-01-25 17:44:30,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d6f578e-407a-4263-9e37-86feea5b401c/GCF_000771085.1_DSM-19703_genomic.fna.gz --refList GCF_000771085.1_DSM-19703_genomic.fna/target_genomes_gtdb.txt --output GCF_000771085.1_DSM-19703_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:41,822] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:41,837] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:41,837] [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_000737845.1	s__Bifidobacterium bombi	99.9685	612	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_014898175.1	s__Bifidobacterium lemurum	77.7326	89	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_012932365.1	s__Bifidobacterium sp012932365	77.7233	87	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898155.1	s__Bifidobacterium eulemuris	77.718	90	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018555635.1	s__Bifidobacterium sp018555635	77.6071	85	615	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	77.6014	103	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_003951095.1	s__Bifidobacterium goeldii	77.5752	56	615	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	77.53	89	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	77.5155	79	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_003129925.1	s__Galliscardovia catulorum	77.5087	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	77.4823	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000010425.1	s__Bifidobacterium adolescentis	77.4746	80	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_002259745.1	s__Bifidobacterium myosotis	77.4465	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	77.4265	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129045.1	s__Bifidobacterium merycicum	77.3555	87	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_001042635.1	s__Bifidobacterium scardovii	77.3506	101	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_002860365.1	s__Bifidobacterium parmae	77.3303	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.3085	88	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009299485.1	s__Bifidobacterium apri	77.2947	82	615	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	77.2924	92	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000771265.1	s__Bifidobacterium thermophilum	77.2339	81	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_000741765.1	s__Bifidobacterium tsurumiense	77.1778	62	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.58	0.98	0.96	4	-
GCF_010667615.1	s__Bifidobacterium choloepi	77.1561	81	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	77.1007	91	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741715.1	s__Bifidobacterium saguini	77.08	68	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_002259755.1	s__Bifidobacterium hapali	76.9409	51	615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:41,840] [INFO] GTDB search result was written to GCF_000771085.1_DSM-19703_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:41,840] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:41,844] [INFO] DFAST_QC result json was written to GCF_000771085.1_DSM-19703_genomic.fna/dqc_result.json
[2024-01-25 17:44:41,844] [INFO] DFAST_QC completed!
[2024-01-25 17:44:41,844] [INFO] Total running time: 0h0m51s