[2024-01-24 12:52:24,997] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,002] [INFO] DQC Reference Directory: /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference
[2024-01-24 12:52:26,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,291] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,292] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb04b30d-bb31-4385-8d24-d4c7c3e8f9df/GCF_004116955.1_ASM411695v1_genomic.fna.gz | prodigal -d GCF_004116955.1_ASM411695v1_genomic.fna/cds.fna -a GCF_004116955.1_ASM411695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:37,662] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:37,662] [INFO] Task started: HMMsearch
[2024-01-24 12:52:37,662] [INFO] Running command: hmmsearch --tblout GCF_004116955.1_ASM411695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/reference_markers.hmm GCF_004116955.1_ASM411695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:37,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:37,988] [INFO] Found 6/6 markers.
[2024-01-24 12:52:38,025] [INFO] Query marker FASTA was written to GCF_004116955.1_ASM411695v1_genomic.fna/markers.fasta
[2024-01-24 12:52:38,026] [INFO] Task started: Blastn
[2024-01-24 12:52:38,026] [INFO] Running command: blastn -query GCF_004116955.1_ASM411695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/reference_markers.fasta -out GCF_004116955.1_ASM411695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:38,659] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:38,664] [INFO] Selected 14 target genomes.
[2024-01-24 12:52:38,665] [INFO] Target genome list was writen to GCF_004116955.1_ASM411695v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:38,678] [INFO] Task started: fastANI
[2024-01-24 12:52:38,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb04b30d-bb31-4385-8d24-d4c7c3e8f9df/GCF_004116955.1_ASM411695v1_genomic.fna.gz --refList GCF_004116955.1_ASM411695v1_genomic.fna/target_genomes.txt --output GCF_004116955.1_ASM411695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:51,901] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:51,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:51,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:51,915] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:52:51,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:51,915] [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 vallismortis	strain=DSM 11031	GCA_004116955.1	72361	72361	type	True	100.0	1421	1428	95	conclusive
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	99.9555	1240	1428	95	conclusive
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	92.4531	1198	1428	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	92.3785	1171	1428	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	92.0816	1210	1428	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	91.998	1201	1428	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	90.6	1210	1428	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	90.4451	988	1428	95	below_threshold
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	77.2096	55	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:51,917] [INFO] DFAST Taxonomy check result was written to GCF_004116955.1_ASM411695v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:51,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:51,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:51,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/checkm_data
[2024-01-24 12:52:51,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:51,960] [INFO] Task started: CheckM
[2024-01-24 12:52:51,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116955.1_ASM411695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116955.1_ASM411695v1_genomic.fna/checkm_input GCF_004116955.1_ASM411695v1_genomic.fna/checkm_result
[2024-01-24 12:53:31,653] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:31,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:31,681] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:31,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:31,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116955.1_ASM411695v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:31,682] [INFO] Task started: Blastn
[2024-01-24 12:53:31,682] [INFO] Running command: blastn -query GCF_004116955.1_ASM411695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2606d54-7a5e-401a-914e-c3426ed426d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116955.1_ASM411695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:32,441] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:32,445] [INFO] Selected 13 target genomes.
[2024-01-24 12:53:32,445] [INFO] Target genome list was writen to GCF_004116955.1_ASM411695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:32,467] [INFO] Task started: fastANI
[2024-01-24 12:53:32,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb04b30d-bb31-4385-8d24-d4c7c3e8f9df/GCF_004116955.1_ASM411695v1_genomic.fna.gz --refList GCF_004116955.1_ASM411695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116955.1_ASM411695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:44,202] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:44,215] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:44,216] [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_004116955.1	s__Bacillus vallismortis	100.0	1419	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	conclusive
GCF_002153395.1	s__Bacillus subtilis_G	93.207	1177	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_000227465.1	s__Bacillus spizizenii	92.4487	1200	1428	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	91.9882	1202	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_004124315.1	s__Bacillus cabrialesii	91.5166	1159	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_000009045.1	s__Bacillus subtilis	90.6123	1212	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_000507145.1	s__Bacillus tequilensis	90.2487	1129	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_001461825.1	s__Bacillus velezensis	80.641	665	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_000196735.1	s__Bacillus amyloliquefaciens	80.6161	654	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.08	97.42	0.94	0.89	27	-
GCF_001584325.1	s__Bacillus nakamurai	80.5865	658	1428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:44,217] [INFO] GTDB search result was written to GCF_004116955.1_ASM411695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:44,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:44,221] [INFO] DFAST_QC result json was written to GCF_004116955.1_ASM411695v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:44,221] [INFO] DFAST_QC completed!
[2024-01-24 12:53:44,222] [INFO] Total running time: 0h1m19s