[2024-01-24 13:32:33,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:33,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:33,601] [INFO] DQC Reference Directory: /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference
[2024-01-24 13:32:34,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:34,976] [INFO] Task started: Prodigal
[2024-01-24 13:32:34,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c5d2f38-3ea1-4d54-8d20-338cb1228ec5/GCF_003581585.1_ASM358158v1_genomic.fna.gz | prodigal -d GCF_003581585.1_ASM358158v1_genomic.fna/cds.fna -a GCF_003581585.1_ASM358158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:46,614] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:46,614] [INFO] Task started: HMMsearch
[2024-01-24 13:32:46,614] [INFO] Running command: hmmsearch --tblout GCF_003581585.1_ASM358158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/reference_markers.hmm GCF_003581585.1_ASM358158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:47,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:47,003] [INFO] Found 6/6 markers.
[2024-01-24 13:32:47,059] [INFO] Query marker FASTA was written to GCF_003581585.1_ASM358158v1_genomic.fna/markers.fasta
[2024-01-24 13:32:47,060] [INFO] Task started: Blastn
[2024-01-24 13:32:47,060] [INFO] Running command: blastn -query GCF_003581585.1_ASM358158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/reference_markers.fasta -out GCF_003581585.1_ASM358158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,729] [INFO] Selected 32 target genomes.
[2024-01-24 13:32:47,729] [INFO] Target genome list was writen to GCF_003581585.1_ASM358158v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,740] [INFO] Task started: fastANI
[2024-01-24 13:32:47,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5d2f38-3ea1-4d54-8d20-338cb1228ec5/GCF_003581585.1_ASM358158v1_genomic.fna.gz --refList GCF_003581585.1_ASM358158v1_genomic.fna/target_genomes.txt --output GCF_003581585.1_ASM358158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:10,353] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:10,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:10,369] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:10,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:10,369] [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 salacetis	strain=SKP7-4	GCA_003581585.1	2315464	2315464	type	True	100.0	1513	1516	95	conclusive
Bacillus enclensis	strain=SGD-1123	GCA_001456935.1	1402860	1402860	type	True	77.6844	201	1516	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_900094975.1	1402860	1402860	type	True	77.6752	201	1516	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.5218	91	1516	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	77.405	124	1516	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.363	53	1516	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	77.2174	66	1516	95	below_threshold
Falsibacillus pallidus	strain=DSM 25281	GCA_003350505.1	493781	493781	type	True	77.1269	125	1516	95	below_threshold
Bacillus massiliglaciei	strain=Marseille-P2600	GCA_900098925.1	1816693	1816693	type	True	77.0994	72	1516	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.9548	90	1516	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	76.9447	78	1516	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	76.9447	78	1516	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	76.9091	79	1516	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	76.9005	62	1516	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	76.8975	81	1516	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	76.8299	60	1516	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	76.7733	68	1516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,371] [INFO] DFAST Taxonomy check result was written to GCF_003581585.1_ASM358158v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:10,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:10,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:10,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/checkm_data
[2024-01-24 13:33:10,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:10,420] [INFO] Task started: CheckM
[2024-01-24 13:33:10,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003581585.1_ASM358158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003581585.1_ASM358158v1_genomic.fna/checkm_input GCF_003581585.1_ASM358158v1_genomic.fna/checkm_result
[2024-01-24 13:33:51,832] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:51,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,858] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:51,859] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:51,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003581585.1_ASM358158v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:51,860] [INFO] Task started: Blastn
[2024-01-24 13:33:51,860] [INFO] Running command: blastn -query GCF_003581585.1_ASM358158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7d6c50f-1223-48af-afc9-19f3ba67efad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003581585.1_ASM358158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:52,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:52,713] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:52,713] [INFO] Target genome list was writen to GCF_003581585.1_ASM358158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:52,743] [INFO] Task started: fastANI
[2024-01-24 13:33:52,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c5d2f38-3ea1-4d54-8d20-338cb1228ec5/GCF_003581585.1_ASM358158v1_genomic.fna.gz --refList GCF_003581585.1_ASM358158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003581585.1_ASM358158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:07,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:07,359] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:07,360] [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_003581585.1	s__Bacillus_BM salacetis	100.0	1513	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003316765.1	s__Bacillus_BM sp003316765	80.2246	709	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.55	98.55	0.89	0.89	2	-
GCF_000181495.1	s__Bacillus_BM sp000181495	80.1966	640	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180615.1	s__Bacillus_BM vietnamensis_A	80.1219	694	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.11	98.11	0.91	0.91	2	-
GCF_008180415.1	s__Bacillus_BM vietnamensis_B	79.9953	708	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563655.1	s__Rossellomorea sp002563655	77.8793	174	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456935.1	s__Rossellomorea enclensis	77.6752	201	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	98.25	97.66	0.91	0.88	7	-
GCF_003668575.1	s__Falsibacillus albus	77.405	124	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960805.1	s__Bacillus_BV sp014960805	77.1201	61	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591465.1	s__Cytobacillus firmus	76.9686	88	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.21	98.02	0.95	0.85	11	-
GCF_001273925.1	s__Bacillus_AZ sp001273925	76.957	78	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708755.2	s__Bacillus_P indicus	76.8975	81	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_000262755.1	s__Bacillus_Z methanolicus	76.7733	68	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002863585.1	s__Bacillus_AI deserti_A	76.7634	73	1516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AI	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:07,362] [INFO] GTDB search result was written to GCF_003581585.1_ASM358158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:07,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:07,366] [INFO] DFAST_QC result json was written to GCF_003581585.1_ASM358158v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:07,366] [INFO] DFAST_QC completed!
[2024-01-24 13:34:07,366] [INFO] Total running time: 0h1m34s