[2024-01-25 20:21:35,383] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference
[2024-01-25 20:21:36,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,531] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg549afc87-bf82-4836-9ff0-fde6a2a1835f/GCF_016909155.1_ASM1690915v1_genomic.fna.gz | prodigal -d GCF_016909155.1_ASM1690915v1_genomic.fna/cds.fna -a GCF_016909155.1_ASM1690915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:42,099] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:42,099] [INFO] Task started: HMMsearch
[2024-01-25 20:21:42,099] [INFO] Running command: hmmsearch --tblout GCF_016909155.1_ASM1690915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/reference_markers.hmm GCF_016909155.1_ASM1690915v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:42,304] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:42,305] [INFO] Found 6/6 markers.
[2024-01-25 20:21:42,329] [INFO] Query marker FASTA was written to GCF_016909155.1_ASM1690915v1_genomic.fna/markers.fasta
[2024-01-25 20:21:42,330] [INFO] Task started: Blastn
[2024-01-25 20:21:42,330] [INFO] Running command: blastn -query GCF_016909155.1_ASM1690915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/reference_markers.fasta -out GCF_016909155.1_ASM1690915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:42,879] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:42,882] [INFO] Selected 29 target genomes.
[2024-01-25 20:21:42,883] [INFO] Target genome list was writen to GCF_016909155.1_ASM1690915v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:42,900] [INFO] Task started: fastANI
[2024-01-25 20:21:42,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg549afc87-bf82-4836-9ff0-fde6a2a1835f/GCF_016909155.1_ASM1690915v1_genomic.fna.gz --refList GCF_016909155.1_ASM1690915v1_genomic.fna/target_genomes.txt --output GCF_016909155.1_ASM1690915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:57,361] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:57,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:57,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:57,374] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:57,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:57,374] [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
Lysinibacillus fusiformis	strain=ATCC 7055	GCA_003049525.1	28031	28031	type	True	78.2752	61	862	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	78.0444	98	862	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	78.0245	86	862	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	77.9367	97	862	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	77.9044	61	862	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	77.9018	97	862	95	below_threshold
Rummeliibacillus stabekisii	strain=DSM 25578	GCA_014202625.1	241244	241244	type	True	77.7429	52	862	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	77.4642	68	862	95	below_threshold
Rummeliibacillus stabekisii	strain=NBRC 104870	GCA_007988965.1	241244	241244	type	True	77.4561	51	862	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_003664125.1	1373	1373	type	True	77.3113	51	862	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	77.3003	69	862	95	below_threshold
Kurthia sibirica	strain=ATCC 49154	GCA_003143975.1	202750	202750	type	True	76.9989	54	862	95	below_threshold
Kurthia sibirica	strain=NBRC 101530	GCA_007989725.1	202750	202750	type	True	76.9557	54	862	95	below_threshold
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	76.9103	70	862	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	76.7493	71	862	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	76.7492	75	862	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	76.5439	61	862	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	76.4554	53	862	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	76.4067	51	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:57,376] [INFO] DFAST Taxonomy check result was written to GCF_016909155.1_ASM1690915v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:57,376] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:57,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:57,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/checkm_data
[2024-01-25 20:21:57,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:57,405] [INFO] Task started: CheckM
[2024-01-25 20:21:57,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909155.1_ASM1690915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909155.1_ASM1690915v1_genomic.fna/checkm_input GCF_016909155.1_ASM1690915v1_genomic.fna/checkm_result
[2024-01-25 20:22:19,803] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:19,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:19,846] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:19,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:19,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909155.1_ASM1690915v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:19,848] [INFO] Task started: Blastn
[2024-01-25 20:22:19,848] [INFO] Running command: blastn -query GCF_016909155.1_ASM1690915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg653d9d9c-bfd3-47a9-b640-924caf427bdc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909155.1_ASM1690915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:20,612] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:20,617] [INFO] Selected 20 target genomes.
[2024-01-25 20:22:20,617] [INFO] Target genome list was writen to GCF_016909155.1_ASM1690915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:20,693] [INFO] Task started: fastANI
[2024-01-25 20:22:20,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg549afc87-bf82-4836-9ff0-fde6a2a1835f/GCF_016909155.1_ASM1690915v1_genomic.fna.gz --refList GCF_016909155.1_ASM1690915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909155.1_ASM1690915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:33,500] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:33,513] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:33,513] [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_016909155.1	s__Chryseomicrobium aureum	100.0	860	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002265435.1	s__Chryseomicrobium hominis	81.5201	431	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798305.1	s__Chryseomicrobium excrementi	81.1482	432	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807035.1	s__Psychrobacillus sp008807035	78.4109	81	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	98.73	98.60	0.95	0.94	4	-
GCF_900111345.1	s__Psychrobacillus sp900111345	78.0338	92	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	78.0078	98	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002237755.1	s__Lysinibacillus sp002237755	77.9094	66	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
GCF_006861825.1	s__Psychrobacillus vulpis	77.9018	97	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168685.1	s__Solibacillus isronensis_A	77.845	75	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004367585.1	s__Paenisporosarcina antarctica	77.8338	70	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	95.47	95.47	0.86	0.86	2	-
GCF_900099655.1	s__Planococcus glaciei	77.4695	61	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.05	96.92	0.90	0.89	5	-
GCF_003991225.1	s__Kurthia intestinigallinarum	77.3401	53	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_001592825.1	s__Planococcus maritimus_C	77.1757	51	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.02	95.52	0.95	0.93	3	-
GCF_000484595.1	s__Paenisporosarcina sp000484595	77.1716	89	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143975.1	s__Kurthia sibirica	76.9989	54	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000285555.1	s__Kurthia massiliensis	76.9103	70	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006539985.1	s__Kurthia gibsonii	76.7493	71	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	-
GCF_004761975.1	s__Planococcus koreensis	76.4067	51	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002551815.1	s__Bacillus_A sp002551815	76.3339	54	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:33,518] [INFO] GTDB search result was written to GCF_016909155.1_ASM1690915v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:33,519] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:33,523] [INFO] DFAST_QC result json was written to GCF_016909155.1_ASM1690915v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:33,523] [INFO] DFAST_QC completed!
[2024-01-25 20:22:33,523] [INFO] Total running time: 0h0m58s