[2024-01-24 13:22:10,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference
[2024-01-24 13:22:11,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,963] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg743ca6d4-3581-4d9f-b155-ad9e6527c94d/GCF_000742895.1_ASM74289v1_genomic.fna.gz | prodigal -d GCF_000742895.1_ASM74289v1_genomic.fna/cds.fna -a GCF_000742895.1_ASM74289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:22,987] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:22,988] [INFO] Task started: HMMsearch
[2024-01-24 13:22:22,988] [INFO] Running command: hmmsearch --tblout GCF_000742895.1_ASM74289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/reference_markers.hmm GCF_000742895.1_ASM74289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:23,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:23,334] [INFO] Found 6/6 markers.
[2024-01-24 13:22:23,393] [INFO] Query marker FASTA was written to GCF_000742895.1_ASM74289v1_genomic.fna/markers.fasta
[2024-01-24 13:22:23,394] [INFO] Task started: Blastn
[2024-01-24 13:22:23,394] [INFO] Running command: blastn -query GCF_000742895.1_ASM74289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/reference_markers.fasta -out GCF_000742895.1_ASM74289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,067] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,070] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:24,071] [INFO] Target genome list was writen to GCF_000742895.1_ASM74289v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:24,080] [INFO] Task started: fastANI
[2024-01-24 13:22:24,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg743ca6d4-3581-4d9f-b155-ad9e6527c94d/GCF_000742895.1_ASM74289v1_genomic.fna.gz --refList GCF_000742895.1_ASM74289v1_genomic.fna/target_genomes.txt --output GCF_000742895.1_ASM74289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:42,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:42,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:42,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:42,347] [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 13:22:42,347] [INFO] Found 14 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:22:42,347] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:42,348] [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 anthracis	strain=Vollum	GCA_000742895.1	1392	1392	type	True	100.0	1834	1834	95	inconclusive
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	99.9971	1827	1834	95	inconclusive
Bacillus anthracis	strain=Vollum	GCA_000167275.1	1392	1392	type	True	99.9855	1793	1834	95	inconclusive
Bacillus anthracis	strain=A0488	GCA_000181835.1	1392	1392	type	True	99.957	1759	1834	95	inconclusive
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	95.2352	1512	1834	95	inconclusive
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	94.7826	1504	1834	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	94.0734	1498	1834	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	93.9907	1356	1834	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	91.8181	1504	1834	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	91.8128	1426	1834	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	91.8107	1511	1834	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	89.6121	1454	1834	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1678	108	1834	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.6361	74	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:42,349] [INFO] DFAST Taxonomy check result was written to GCF_000742895.1_ASM74289v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:42,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:42,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:42,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/checkm_data
[2024-01-24 13:22:42,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:42,413] [INFO] Task started: CheckM
[2024-01-24 13:22:42,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000742895.1_ASM74289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000742895.1_ASM74289v1_genomic.fna/checkm_input GCF_000742895.1_ASM74289v1_genomic.fna/checkm_result
[2024-01-24 13:23:19,117] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:19,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:19,147] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:19,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:19,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000742895.1_ASM74289v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:19,148] [INFO] Task started: Blastn
[2024-01-24 13:23:19,149] [INFO] Running command: blastn -query GCF_000742895.1_ASM74289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168eb59-ebbb-4587-8aa9-caaa4b3c1144/dqc_reference/reference_markers_gtdb.fasta -out GCF_000742895.1_ASM74289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:19,931] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:19,936] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:19,936] [INFO] Target genome list was writen to GCF_000742895.1_ASM74289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:19,954] [INFO] Task started: fastANI
[2024-01-24 13:23:19,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg743ca6d4-3581-4d9f-b155-ad9e6527c94d/GCF_000742895.1_ASM74289v1_genomic.fna.gz --refList GCF_000742895.1_ASM74289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000742895.1_ASM74289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:37,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:37,227] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:37,227] [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_000742895.1	s__Bacillus_A anthracis	100.0	1834	1834	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	conclusive
GCF_001883995.1	s__Bacillus_A paranthracis	95.2352	1512	1834	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	-
GCF_001884035.1	s__Bacillus_A tropicus	94.7777	1504	1834	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_001455345.1	s__Bacillus_A thuringiensis_N	94.1246	1557	1834	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_018332475.1	s__Bacillus_A sp018332475	93.9845	1357	1834	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_006494425.1	s__Bacillus_A sp006494425	93.9733	1583	1834	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	93.5088	1527	1834	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_002571225.1	s__Bacillus_A sp002571225	93.3327	1519	1834	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	93.2843	1443	1834	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_001583695.1	s__Bacillus_A wiedmannii	93.1307	1484	1834	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_008923725.1	s__Bacillus_A sp008923725	93.0576	1484	1834	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_002567495.1	s__Bacillus_A cereus_AQ	91.1699	1454	1834	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_014932895.1	s__Bacillus_A thuringiensis_AA	90.3059	1403	1834	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:37,229] [INFO] GTDB search result was written to GCF_000742895.1_ASM74289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:37,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:37,233] [INFO] DFAST_QC result json was written to GCF_000742895.1_ASM74289v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:37,233] [INFO] DFAST_QC completed!
[2024-01-24 13:23:37,233] [INFO] Total running time: 0h1m27s