[2024-01-25 20:17:20,799] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:20,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:20,800] [INFO] DQC Reference Directory: /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference
[2024-01-25 20:17:21,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:21,906] [INFO] Task started: Prodigal
[2024-01-25 20:17:21,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg33344f1f-452b-47cb-b183-08e43fa2ebdd/GCF_016909175.1_ASM1690917v1_genomic.fna.gz | prodigal -d GCF_016909175.1_ASM1690917v1_genomic.fna/cds.fna -a GCF_016909175.1_ASM1690917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:29,734] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:29,734] [INFO] Task started: HMMsearch
[2024-01-25 20:17:29,734] [INFO] Running command: hmmsearch --tblout GCF_016909175.1_ASM1690917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/reference_markers.hmm GCF_016909175.1_ASM1690917v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:29,971] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:29,973] [INFO] Found 6/6 markers.
[2024-01-25 20:17:30,005] [INFO] Query marker FASTA was written to GCF_016909175.1_ASM1690917v1_genomic.fna/markers.fasta
[2024-01-25 20:17:30,005] [INFO] Task started: Blastn
[2024-01-25 20:17:30,006] [INFO] Running command: blastn -query GCF_016909175.1_ASM1690917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/reference_markers.fasta -out GCF_016909175.1_ASM1690917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:30,557] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:30,560] [INFO] Selected 25 target genomes.
[2024-01-25 20:17:30,560] [INFO] Target genome list was writen to GCF_016909175.1_ASM1690917v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:30,580] [INFO] Task started: fastANI
[2024-01-25 20:17:30,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg33344f1f-452b-47cb-b183-08e43fa2ebdd/GCF_016909175.1_ASM1690917v1_genomic.fna.gz --refList GCF_016909175.1_ASM1690917v1_genomic.fna/target_genomes.txt --output GCF_016909175.1_ASM1690917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:49,886] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:49,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:49,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:49,899] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:49,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:49,900] [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
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	100.0	1428	1432	95	conclusive
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	78.2709	319	1432	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	78.0549	60	1432	95	below_threshold
Peribacillus butanolivorans	strain=DSM 18926	GCA_001273755.1	421767	421767	type	True	77.6795	138	1432	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	77.6072	79	1432	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.5479	82	1432	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.5102	114	1432	95	below_threshold
Bacillus tropicus	strain=N24	GCA_001884035.1	2026188	2026188	type	True	77.5021	51	1432	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	77.428	106	1432	95	below_threshold
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	77.2935	72	1432	95	below_threshold
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	77.2772	68	1432	95	below_threshold
Mesobacillus harenae	strain=Y40	GCA_013343715.1	2213203	2213203	type	True	77.1721	99	1432	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_000007825.1	1396	1396	suspected-type	True	77.1573	60	1432	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.1227	63	1432	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.0983	82	1432	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.0487	86	1432	95	below_threshold
Bacillus proteolyticus	strain=TD42	GCA_001884065.1	2026192	2026192	type	True	76.9626	55	1432	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.9221	115	1432	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	76.8882	70	1432	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	76.8601	95	1432	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.8565	71	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:49,901] [INFO] DFAST Taxonomy check result was written to GCF_016909175.1_ASM1690917v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:49,904] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:49,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:49,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/checkm_data
[2024-01-25 20:17:49,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:49,948] [INFO] Task started: CheckM
[2024-01-25 20:17:49,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909175.1_ASM1690917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909175.1_ASM1690917v1_genomic.fna/checkm_input GCF_016909175.1_ASM1690917v1_genomic.fna/checkm_result
[2024-01-25 20:18:17,772] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:17,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:17,794] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:17,794] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:17,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909175.1_ASM1690917v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:17,796] [INFO] Task started: Blastn
[2024-01-25 20:18:17,796] [INFO] Running command: blastn -query GCF_016909175.1_ASM1690917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge038d289-0716-4a5d-bb87-d079c1be30c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909175.1_ASM1690917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:18,572] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:18,582] [INFO] Selected 23 target genomes.
[2024-01-25 20:18:18,582] [INFO] Target genome list was writen to GCF_016909175.1_ASM1690917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:18,605] [INFO] Task started: fastANI
[2024-01-25 20:18:18,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg33344f1f-452b-47cb-b183-08e43fa2ebdd/GCF_016909175.1_ASM1690917v1_genomic.fna.gz --refList GCF_016909175.1_ASM1690917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909175.1_ASM1690917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:37,019] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:37,032] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:37,032] [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_016909175.1	s__Bacillus_AI deserti	100.0	1428	1432	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	conclusive
GCF_002863585.1	s__Bacillus_AI deserti_A	82.4974	962	1432	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	-
GCF_000430765.1	s__Bacillus_AI kribbensis	78.244	320	1432	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	-
GCF_003429095.1	s__Peribacillus_A saganii	77.7235	144	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613035.1	s__Cytobacillus sp018613035	77.6202	101	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_019039215.1	s__Cytobacillus sp019039215	77.5071	94	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724485.1	s__Bacillus_Z methanolicus_A	77.4948	92	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003073175.1	s__Bacillus_BN acanthi	77.4521	107	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009466385.1	s__Bacillus_BN tepidiphilus	77.4512	109	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018742245.1	s__Bacillus_A cereus_U	77.4325	56	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.53	95.81	0.88	0.84	34	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	77.3846	115	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103525.1	s__Neobacillus sp900103525	77.3212	86	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343665.1	s__Cytobacillus sp018343665	77.2678	96	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182355.1	s__Cytobacillus oceanisediminis_A	77.1413	124	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928415.1	s__Neobacillus sp009928415	77.0037	123	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009849585.1	s__Cytobacillus sp009849585	76.9867	112	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975175.1	s__Bacillus_A sp002975175	76.913	51	1432	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_016908975.1	s__Neobacillus cucumis	76.907	114	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518885.1	s__Cytobacillus sp000518885	76.8602	123	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262755.1	s__Bacillus_Z methanolicus	76.7761	84	1432	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_012163115.1	s__Mesobacillus selenatarsenatis_A	76.7739	84	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765675.1	s__Neobacillus sp016765675	76.7587	65	1432	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:37,033] [INFO] GTDB search result was written to GCF_016909175.1_ASM1690917v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:37,035] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:37,038] [INFO] DFAST_QC result json was written to GCF_016909175.1_ASM1690917v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:37,038] [INFO] DFAST_QC completed!
[2024-01-25 20:18:37,038] [INFO] Total running time: 0h1m16s