[2024-01-24 13:40:43,223] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference
[2024-01-24 13:40:44,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,616] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgabfefd55-073c-4c4f-8cc1-019093372cd1/GCF_018390475.2_ASM1839047v2_genomic.fna.gz | prodigal -d GCF_018390475.2_ASM1839047v2_genomic.fna/cds.fna -a GCF_018390475.2_ASM1839047v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,019] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,019] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,019] [INFO] Running command: hmmsearch --tblout GCF_018390475.2_ASM1839047v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/reference_markers.hmm GCF_018390475.2_ASM1839047v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,366] [INFO] Found 6/6 markers.
[2024-01-24 13:40:57,417] [INFO] Query marker FASTA was written to GCF_018390475.2_ASM1839047v2_genomic.fna/markers.fasta
[2024-01-24 13:40:57,417] [INFO] Task started: Blastn
[2024-01-24 13:40:57,418] [INFO] Running command: blastn -query GCF_018390475.2_ASM1839047v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/reference_markers.fasta -out GCF_018390475.2_ASM1839047v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,111] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:58,111] [INFO] Target genome list was writen to GCF_018390475.2_ASM1839047v2_genomic.fna/target_genomes.txt
[2024-01-24 13:40:58,116] [INFO] Task started: fastANI
[2024-01-24 13:40:58,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgabfefd55-073c-4c4f-8cc1-019093372cd1/GCF_018390475.2_ASM1839047v2_genomic.fna.gz --refList GCF_018390475.2_ASM1839047v2_genomic.fna/target_genomes.txt --output GCF_018390475.2_ASM1839047v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:09,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:09,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:09,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:09,467] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:09,467] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:09,467] [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
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	93.3529	1285	1431	95	below_threshold
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	93.3187	1273	1431	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	93.3002	1263	1431	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	93.2734	1038	1431	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	93.2432	1251	1431	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	93.1864	1185	1431	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	92.178	1274	1431	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	92.1628	1278	1431	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	91.275	1067	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,469] [INFO] DFAST Taxonomy check result was written to GCF_018390475.2_ASM1839047v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:09,469] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:09,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:09,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/checkm_data
[2024-01-24 13:41:09,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:09,521] [INFO] Task started: CheckM
[2024-01-24 13:41:09,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018390475.2_ASM1839047v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018390475.2_ASM1839047v2_genomic.fna/checkm_input GCF_018390475.2_ASM1839047v2_genomic.fna/checkm_result
[2024-01-24 13:41:53,144] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:53,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:53,168] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:53,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:53,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018390475.2_ASM1839047v2_genomic.fna/markers.fasta)
[2024-01-24 13:41:53,169] [INFO] Task started: Blastn
[2024-01-24 13:41:53,169] [INFO] Running command: blastn -query GCF_018390475.2_ASM1839047v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcefb118e-73e6-4992-9060-67634493a516/dqc_reference/reference_markers_gtdb.fasta -out GCF_018390475.2_ASM1839047v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,997] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:53,997] [INFO] Target genome list was writen to GCF_018390475.2_ASM1839047v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:54,009] [INFO] Task started: fastANI
[2024-01-24 13:41:54,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgabfefd55-073c-4c4f-8cc1-019093372cd1/GCF_018390475.2_ASM1839047v2_genomic.fna.gz --refList GCF_018390475.2_ASM1839047v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018390475.2_ASM1839047v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:02,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:02,436] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:02,436] [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_004124315.1	s__Bacillus cabrialesii	96.6439	1266	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	conclusive
GCF_000227465.1	s__Bacillus spizizenii	93.3419	1272	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCA_000332645.1	s__Bacillus inaquosorum	93.3002	1263	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_000507145.1	s__Bacillus tequilensis	93.1864	1185	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_002153395.1	s__Bacillus subtilis_G	92.3186	1220	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_000009045.1	s__Bacillus subtilis	92.1447	1292	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_004116955.1	s__Bacillus vallismortis	91.3924	1179	1431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,438] [INFO] GTDB search result was written to GCF_018390475.2_ASM1839047v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:02,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:02,442] [INFO] DFAST_QC result json was written to GCF_018390475.2_ASM1839047v2_genomic.fna/dqc_result.json
[2024-01-24 13:42:02,442] [INFO] DFAST_QC completed!
[2024-01-24 13:42:02,442] [INFO] Total running time: 0h1m19s