[2024-01-24 11:12:35,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:35,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:35,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference
[2024-01-24 11:12:37,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:37,029] [INFO] Task started: Prodigal
[2024-01-24 11:12:37,029] [INFO] Running command: gunzip -c /var/lib/cwl/stgb10afe2a-1e3e-4967-b3e3-d3c3d4e87d6d/GCF_001883995.1_ASM188399v1_genomic.fna.gz | prodigal -d GCF_001883995.1_ASM188399v1_genomic.fna/cds.fna -a GCF_001883995.1_ASM188399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,413] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,414] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,414] [INFO] Running command: hmmsearch --tblout GCF_001883995.1_ASM188399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/reference_markers.hmm GCF_001883995.1_ASM188399v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:47,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:47,765] [INFO] Found 6/6 markers.
[2024-01-24 11:12:47,821] [INFO] Query marker FASTA was written to GCF_001883995.1_ASM188399v1_genomic.fna/markers.fasta
[2024-01-24 11:12:47,822] [INFO] Task started: Blastn
[2024-01-24 11:12:47,822] [INFO] Running command: blastn -query GCF_001883995.1_ASM188399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/reference_markers.fasta -out GCF_001883995.1_ASM188399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,442] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,445] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:48,445] [INFO] Target genome list was writen to GCF_001883995.1_ASM188399v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,451] [INFO] Task started: fastANI
[2024-01-24 11:12:48,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10afe2a-1e3e-4967-b3e3-d3c3d4e87d6d/GCF_001883995.1_ASM188399v1_genomic.fna.gz --refList GCF_001883995.1_ASM188399v1_genomic.fna/target_genomes.txt --output GCF_001883995.1_ASM188399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:06,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:06,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:06,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:06,395] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {1392: 'Bacillus anthracis', 1396: 'Bacillus cereus', 1428: 'Bacillus thuringiensis'}, {}
[2024-01-24 11:13:06,395] [INFO] Found 15 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 11:13:06,395] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:13:06,396] [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 paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	100.0	1797	1798	95	inconclusive
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	95.8679	1475	1798	95	inconclusive
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	95.3748	1475	1798	95	inconclusive
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	95.2743	1517	1798	95	inconclusive
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	95.2538	1496	1798	95	inconclusive
Bacillus anthracis	strain=Vollum	GCA_000742895.1	1392	1392	type	True	95.2518	1521	1798	95	inconclusive
Bacillus anthracis	strain=A0488	GCA_000181835.1	1392	1392	type	True	95.2026	1459	1798	95	inconclusive
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	93.754	1311	1798	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	91.9616	1417	1798	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	91.8958	1473	1798	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	89.5089	1416	1798	95	below_threshold
Bacillus clarus	strain=PS00077A	GCA_003428195.1	2338372	2338372	type	True	85.9783	1246	1798	95	below_threshold
Bacillus clarus	strain=BHP	GCA_000746925.1	2338372	2338372	type	True	85.9473	1272	1798	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.6146	109	1798	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.1682	80	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,397] [INFO] DFAST Taxonomy check result was written to GCF_001883995.1_ASM188399v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:06,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:06,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:06,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/checkm_data
[2024-01-24 11:13:06,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:06,458] [INFO] Task started: CheckM
[2024-01-24 11:13:06,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001883995.1_ASM188399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001883995.1_ASM188399v1_genomic.fna/checkm_input GCF_001883995.1_ASM188399v1_genomic.fna/checkm_result
[2024-01-24 11:13:42,856] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:42,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:42,883] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:42,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:42,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001883995.1_ASM188399v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:42,885] [INFO] Task started: Blastn
[2024-01-24 11:13:42,885] [INFO] Running command: blastn -query GCF_001883995.1_ASM188399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaeb57dd-0d60-4074-99ac-a0121b87185c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001883995.1_ASM188399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:43,733] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:43,741] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:43,742] [INFO] Target genome list was writen to GCF_001883995.1_ASM188399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:43,754] [INFO] Task started: fastANI
[2024-01-24 11:13:43,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10afe2a-1e3e-4967-b3e3-d3c3d4e87d6d/GCF_001883995.1_ASM188399v1_genomic.fna.gz --refList GCF_001883995.1_ASM188399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001883995.1_ASM188399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:05,075] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:05,089] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:05,090] [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_001883995.1	s__Bacillus_A paranthracis	100.0	1797	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	97.40	95.70	0.86	0.80	231	conclusive
GCF_001884035.1	s__Bacillus_A tropicus	95.3624	1476	1798	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_000742895.1	s__Bacillus_A anthracis	95.2382	1522	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.2518	99.29	95.34	0.96	0.83	417	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	94.0762	1483	1798	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_006494425.1	s__Bacillus_A sp006494425	93.9965	1513	1798	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_018332475.1	s__Bacillus_A sp018332475	93.754	1311	1798	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	93.4989	1456	1798	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	93.39	1475	1798	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_002746455.1	s__Bacillus_A fungorum	93.3737	1402	1798	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_900094905.1	s__Bacillus_A cereus_AG	93.1895	1473	1798	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_001583695.1	s__Bacillus_A wiedmannii	93.1071	1465	1798	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	-
GCF_001884045.1	s__Bacillus_A mobilis	92.9858	1468	1798	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	-
GCF_008923725.1	s__Bacillus_A sp008923725	92.9535	1438	1798	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_002200015.1	s__Bacillus_A cereus_AZ	91.9362	1419	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.9563	N/A	N/A	N/A	N/A	1	-
GCF_000007825.1	s__Bacillus_A cereus	91.9101	1472	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.55	97.64	0.91	0.84	235	-
GCF_002567495.1	s__Bacillus_A cereus_AQ	91.2433	1460	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.10	96.80	0.92	0.88	3	-
GCF_000746925.1	s__Bacillus_A clarus	85.9633	1270	1798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:05,091] [INFO] GTDB search result was written to GCF_001883995.1_ASM188399v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:05,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:05,096] [INFO] DFAST_QC result json was written to GCF_001883995.1_ASM188399v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:05,096] [INFO] DFAST_QC completed!
[2024-01-24 11:14:05,096] [INFO] Total running time: 0h1m29s