[2024-01-24 15:02:23,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference
[2024-01-24 15:02:24,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,484] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg33b59497-5c2e-4905-b5d4-ce6c40ee524e/GCF_009649735.1_ASM964973v1_genomic.fna.gz | prodigal -d GCF_009649735.1_ASM964973v1_genomic.fna/cds.fna -a GCF_009649735.1_ASM964973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:32,180] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:32,180] [INFO] Task started: HMMsearch
[2024-01-24 15:02:32,180] [INFO] Running command: hmmsearch --tblout GCF_009649735.1_ASM964973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/reference_markers.hmm GCF_009649735.1_ASM964973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:32,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:32,444] [INFO] Found 6/6 markers.
[2024-01-24 15:02:32,478] [INFO] Query marker FASTA was written to GCF_009649735.1_ASM964973v1_genomic.fna/markers.fasta
[2024-01-24 15:02:32,479] [INFO] Task started: Blastn
[2024-01-24 15:02:32,479] [INFO] Running command: blastn -query GCF_009649735.1_ASM964973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/reference_markers.fasta -out GCF_009649735.1_ASM964973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:33,073] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:33,080] [INFO] Selected 30 target genomes.
[2024-01-24 15:02:33,081] [INFO] Target genome list was writen to GCF_009649735.1_ASM964973v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:33,222] [INFO] Task started: fastANI
[2024-01-24 15:02:33,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b59497-5c2e-4905-b5d4-ce6c40ee524e/GCF_009649735.1_ASM964973v1_genomic.fna.gz --refList GCF_009649735.1_ASM964973v1_genomic.fna/target_genomes.txt --output GCF_009649735.1_ASM964973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:52,734] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:52,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:52,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:52,746] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:52,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:52,747] [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
Salinibacillus xinjiangensis	strain=J4	GCA_009649735.1	1229268	1229268	type	True	100.0	1230	1231	95	conclusive
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.8809	54	1231	95	below_threshold
Salinibacillus kushneri	strain=CGMCC 1.3566	GCA_900111405.1	237682	237682	type	True	77.7329	251	1231	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	77.399	52	1231	95	below_threshold
Tenuibacillus multivorans	strain=NBRC 100370	GCA_007989445.1	237069	237069	type	True	77.3892	50	1231	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.041	67	1231	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	76.9253	64	1231	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.8699	62	1231	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.8262	64	1231	95	below_threshold
Pontibacillus yanchengensis	strain=Y32	GCA_000770635.1	462910	462910	type	True	76.8163	58	1231	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.6723	59	1231	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.6576	56	1231	95	below_threshold
Pontibacillus litoralis	strain=JSM 072002	GCA_000775615.1	516703	516703	type	True	76.1272	75	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:52,749] [INFO] DFAST Taxonomy check result was written to GCF_009649735.1_ASM964973v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:52,749] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:52,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:52,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/checkm_data
[2024-01-24 15:02:52,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:52,796] [INFO] Task started: CheckM
[2024-01-24 15:02:52,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649735.1_ASM964973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649735.1_ASM964973v1_genomic.fna/checkm_input GCF_009649735.1_ASM964973v1_genomic.fna/checkm_result
[2024-01-24 15:03:22,989] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:22,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:23,076] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:23,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:23,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649735.1_ASM964973v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:23,078] [INFO] Task started: Blastn
[2024-01-24 15:03:23,078] [INFO] Running command: blastn -query GCF_009649735.1_ASM964973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbcccbb5-07d9-4f13-9222-cd731d703ee1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649735.1_ASM964973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:24,205] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:24,208] [INFO] Selected 28 target genomes.
[2024-01-24 15:03:24,209] [INFO] Target genome list was writen to GCF_009649735.1_ASM964973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:24,245] [INFO] Task started: fastANI
[2024-01-24 15:03:24,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b59497-5c2e-4905-b5d4-ce6c40ee524e/GCF_009649735.1_ASM964973v1_genomic.fna.gz --refList GCF_009649735.1_ASM964973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649735.1_ASM964973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:42,673] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:42,686] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:42,686] [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_009649735.1	s__Salinibacillus xinjiangensis	100.0	1230	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010092505.1	s__Salinibacillus sp010092505	78.251	200	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.9684	55	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_900111405.1	s__Salinibacillus kushneri	77.7452	250	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858175.1	s__Pontibacillus sp009858175	77.7126	63	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.5556	63	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402015.1	s__Filobacillus milosensis	77.4271	66	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Filobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240405.1	s__OEQK01 sp900240405	77.2793	149	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__OEQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.2769	72	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	77.076	65	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770635.1	s__Pontibacillus yanchengensis	76.8163	58	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	76.8124	50	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_009856295.1	s__Pontibacillus yanchengensis_A	76.6623	62	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	99.50	99.50	0.96	0.96	2	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.6586	56	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_017873675.1	s__Lentibacillus litoralis	76.65	57	1231	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:42,690] [INFO] GTDB search result was written to GCF_009649735.1_ASM964973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:42,691] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:42,695] [INFO] DFAST_QC result json was written to GCF_009649735.1_ASM964973v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:42,695] [INFO] DFAST_QC completed!
[2024-01-24 15:03:42,695] [INFO] Total running time: 0h1m19s