[2024-01-24 12:46:35,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference
[2024-01-24 12:46:36,491] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,492] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,492] [INFO] Running command: gunzip -c /var/lib/cwl/stgd62c0c1d-a4a6-4711-85ca-5e0721ebdf7a/GCF_010667645.1_ASM1066764v1_genomic.fna.gz | prodigal -d GCF_010667645.1_ASM1066764v1_genomic.fna/cds.fna -a GCF_010667645.1_ASM1066764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:44,548] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:44,549] [INFO] Task started: HMMsearch
[2024-01-24 12:46:44,549] [INFO] Running command: hmmsearch --tblout GCF_010667645.1_ASM1066764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/reference_markers.hmm GCF_010667645.1_ASM1066764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:44,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:44,726] [INFO] Found 6/6 markers.
[2024-01-24 12:46:44,750] [INFO] Query marker FASTA was written to GCF_010667645.1_ASM1066764v1_genomic.fna/markers.fasta
[2024-01-24 12:46:44,750] [INFO] Task started: Blastn
[2024-01-24 12:46:44,750] [INFO] Running command: blastn -query GCF_010667645.1_ASM1066764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/reference_markers.fasta -out GCF_010667645.1_ASM1066764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:45,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:45,821] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:45,822] [INFO] Target genome list was writen to GCF_010667645.1_ASM1066764v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:45,838] [INFO] Task started: fastANI
[2024-01-24 12:46:45,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgd62c0c1d-a4a6-4711-85ca-5e0721ebdf7a/GCF_010667645.1_ASM1066764v1_genomic.fna.gz --refList GCF_010667645.1_ASM1066764v1_genomic.fna/target_genomes.txt --output GCF_010667645.1_ASM1066764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:54,321] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:54,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:54,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:54,334] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:54,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:54,334] [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 platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	100.0	857	859	95	conclusive
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	90.5004	633	859	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	90.3188	654	859	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	87.3654	571	859	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	87.2291	586	859	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	87.2016	581	859	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	86.4124	556	859	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	84.0746	511	859	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	84.0304	536	859	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	83.527	477	859	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	83.4834	474	859	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.0948	317	859	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.5631	186	859	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5405	159	859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:54,336] [INFO] DFAST Taxonomy check result was written to GCF_010667645.1_ASM1066764v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:54,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:54,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:54,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/checkm_data
[2024-01-24 12:46:54,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:54,364] [INFO] Task started: CheckM
[2024-01-24 12:46:54,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010667645.1_ASM1066764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010667645.1_ASM1066764v1_genomic.fna/checkm_input GCF_010667645.1_ASM1066764v1_genomic.fna/checkm_result
[2024-01-24 12:47:22,564] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:22,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:22,582] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:22,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:22,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010667645.1_ASM1066764v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:22,583] [INFO] Task started: Blastn
[2024-01-24 12:47:22,583] [INFO] Running command: blastn -query GCF_010667645.1_ASM1066764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc412d23-ba9e-4b2f-91d1-08c946e89f8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_010667645.1_ASM1066764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:24,244] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:24,249] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:24,250] [INFO] Target genome list was writen to GCF_010667645.1_ASM1066764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:24,256] [INFO] Task started: fastANI
[2024-01-24 12:47:24,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgd62c0c1d-a4a6-4711-85ca-5e0721ebdf7a/GCF_010667645.1_ASM1066764v1_genomic.fna.gz --refList GCF_010667645.1_ASM1066764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010667645.1_ASM1066764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:30,640] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,651] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:30,651] [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_010667645.1	s__Bifidobacterium platyrrhinorum	100.0	857	859	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_002860365.1	s__Bifidobacterium parmae	90.4894	634	859	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	90.3084	655	859	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	87.4028	569	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	87.3816	583	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	87.2396	585	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	86.4337	555	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_000741175.1	s__Bifidobacterium callitrichos	85.9992	576	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_012932365.1	s__Bifidobacterium sp012932365	83.6825	463	859	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	83.6551	472	859	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,653] [INFO] GTDB search result was written to GCF_010667645.1_ASM1066764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:30,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:30,656] [INFO] DFAST_QC result json was written to GCF_010667645.1_ASM1066764v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:30,657] [INFO] DFAST_QC completed!
[2024-01-24 12:47:30,657] [INFO] Total running time: 0h0m55s