[2024-01-24 11:26:03,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,004] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference
[2024-01-24 11:26:04,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,129] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,130] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf92cd78-87a1-48a2-8b5a-8b2bd0e84e02/GCF_018332495.1_ASM1833249v1_genomic.fna.gz | prodigal -d GCF_018332495.1_ASM1833249v1_genomic.fna/cds.fna -a GCF_018332495.1_ASM1833249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:13,648] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:13,649] [INFO] Task started: HMMsearch
[2024-01-24 11:26:13,649] [INFO] Running command: hmmsearch --tblout GCF_018332495.1_ASM1833249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/reference_markers.hmm GCF_018332495.1_ASM1833249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:13,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:13,912] [INFO] Found 6/6 markers.
[2024-01-24 11:26:13,957] [INFO] Query marker FASTA was written to GCF_018332495.1_ASM1833249v1_genomic.fna/markers.fasta
[2024-01-24 11:26:13,957] [INFO] Task started: Blastn
[2024-01-24 11:26:13,958] [INFO] Running command: blastn -query GCF_018332495.1_ASM1833249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/reference_markers.fasta -out GCF_018332495.1_ASM1833249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:14,545] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:14,548] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:14,548] [INFO] Target genome list was writen to GCF_018332495.1_ASM1833249v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:14,587] [INFO] Task started: fastANI
[2024-01-24 11:26:14,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf92cd78-87a1-48a2-8b5a-8b2bd0e84e02/GCF_018332495.1_ASM1833249v1_genomic.fna.gz --refList GCF_018332495.1_ASM1833249v1_genomic.fna/target_genomes.txt --output GCF_018332495.1_ASM1833249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:31,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:31,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:31,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:31,246] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:31,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:31,246] [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 sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	94.5627	1234	1571	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	93.5387	1289	1571	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	93.4553	1266	1571	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	93.1929	1236	1571	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	92.9927	1290	1571	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	92.9845	1273	1571	95	below_threshold
Bacillus luti	strain=TD41	GCA_001884105.1	2026191	2026191	type	True	91.5888	1204	1571	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	91.3969	1279	1571	95	below_threshold
Bacillus toyonensis	strain=BCT-7112	GCA_000496285.1	155322	155322	type	True	91.2177	1216	1571	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	90.9734	1226	1571	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	90.3969	1213	1571	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	90.3431	1237	1571	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	90.2893	1214	1571	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	90.1973	1231	1571	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.4051	96	1571	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.5428	55	1571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:31,248] [INFO] DFAST Taxonomy check result was written to GCF_018332495.1_ASM1833249v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:31,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:31,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:31,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/checkm_data
[2024-01-24 11:26:31,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:31,304] [INFO] Task started: CheckM
[2024-01-24 11:26:31,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018332495.1_ASM1833249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018332495.1_ASM1833249v1_genomic.fna/checkm_input GCF_018332495.1_ASM1833249v1_genomic.fna/checkm_result
[2024-01-24 11:27:04,383] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:04,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:04,411] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:04,412] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:04,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018332495.1_ASM1833249v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:04,412] [INFO] Task started: Blastn
[2024-01-24 11:27:04,412] [INFO] Running command: blastn -query GCF_018332495.1_ASM1833249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3f6880-62ca-4082-afc3-0c44caafe682/dqc_reference/reference_markers_gtdb.fasta -out GCF_018332495.1_ASM1833249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:05,186] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:05,189] [INFO] Selected 14 target genomes.
[2024-01-24 11:27:05,189] [INFO] Target genome list was writen to GCF_018332495.1_ASM1833249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:05,216] [INFO] Task started: fastANI
[2024-01-24 11:27:05,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf92cd78-87a1-48a2-8b5a-8b2bd0e84e02/GCF_018332495.1_ASM1833249v1_genomic.fna.gz --refList GCF_018332495.1_ASM1833249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018332495.1_ASM1833249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:20,793] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:20,805] [INFO] Found 14 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:27:20,805] [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_001884045.1	s__Bacillus_A mobilis	95.9265	1319	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.91	95.80	0.85	0.81	33	inconclusive
GCF_001583695.1	s__Bacillus_A wiedmannii	95.0635	1255	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.52	95.09	0.90	0.85	225	inconclusive
GCF_008923725.1	s__Bacillus_A sp008923725	94.7945	1274	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900094905.1	s__Bacillus_A cereus_AG	94.7251	1258	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.51	99.13	0.92	0.90	3	-
GCF_018332475.1	s__Bacillus_A sp018332475	94.5627	1234	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	95.31	95.31	0.87	0.87	2	-
GCF_002571225.1	s__Bacillus_A sp002571225	94.0401	1284	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884185.1	s__Bacillus_A albus	93.9958	1280	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.54	95.46	0.90	0.83	25	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	93.6972	1287	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_001884035.1	s__Bacillus_A tropicus	93.4553	1266	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	96.52	95.65	0.91	0.83	109	-
GCF_006494425.1	s__Bacillus_A sp006494425	93.3461	1284	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002746455.1	s__Bacillus_A fungorum	93.2619	1242	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.51	97.51	0.90	0.90	2	-
GCF_001884105.1	s__Bacillus_A luti	91.5888	1204	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.24	95.75	0.91	0.89	10	-
GCF_002584985.1	s__Bacillus_A sp002584985	90.8422	1158	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.52	99.41	0.96	0.94	8	-
GCF_001884065.1	s__Bacillus_A proteolyticus	90.3839	1214	1571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.1182	98.61	98.37	0.91	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,807] [INFO] GTDB search result was written to GCF_018332495.1_ASM1833249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:20,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:20,810] [INFO] DFAST_QC result json was written to GCF_018332495.1_ASM1833249v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:20,811] [INFO] DFAST_QC completed!
[2024-01-24 11:27:20,811] [INFO] Total running time: 0h1m18s