[2024-01-24 15:18:26,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference
[2024-01-24 15:18:28,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,128] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg5400c574-0842-497b-9ae2-f4594527ec95/GCF_016908565.1_ASM1690856v1_genomic.fna.gz | prodigal -d GCF_016908565.1_ASM1690856v1_genomic.fna/cds.fna -a GCF_016908565.1_ASM1690856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:39,326] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:39,326] [INFO] Task started: HMMsearch
[2024-01-24 15:18:39,326] [INFO] Running command: hmmsearch --tblout GCF_016908565.1_ASM1690856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/reference_markers.hmm GCF_016908565.1_ASM1690856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:39,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:39,702] [INFO] Found 6/6 markers.
[2024-01-24 15:18:39,744] [INFO] Query marker FASTA was written to GCF_016908565.1_ASM1690856v1_genomic.fna/markers.fasta
[2024-01-24 15:18:39,745] [INFO] Task started: Blastn
[2024-01-24 15:18:39,745] [INFO] Running command: blastn -query GCF_016908565.1_ASM1690856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/reference_markers.fasta -out GCF_016908565.1_ASM1690856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:40,499] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:40,503] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:40,503] [INFO] Target genome list was writen to GCF_016908565.1_ASM1690856v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:40,510] [INFO] Task started: fastANI
[2024-01-24 15:18:40,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg5400c574-0842-497b-9ae2-f4594527ec95/GCF_016908565.1_ASM1690856v1_genomic.fna.gz --refList GCF_016908565.1_ASM1690856v1_genomic.fna/target_genomes.txt --output GCF_016908565.1_ASM1690856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:56,055] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:56,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:56,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:56,069] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:56,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:56,070] [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
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	79.7828	499	1391	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	79.296	375	1391	95	below_threshold
Bacillus alkalisoli	strain=FJAT-45122	GCA_002797415.1	2011008	2011008	type	True	77.9607	151	1391	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	77.1841	75	1391	95	below_threshold
Metabacillus lacus	strain=KCTC 33946	GCA_009674805.1	1983721	1983721	type	True	77.1668	73	1391	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	77.075	90	1391	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	76.9426	88	1391	95	below_threshold
Bacillus pakistanensis	strain=DSM 24834	GCA_016908495.1	992288	992288	type	True	76.895	68	1391	95	below_threshold
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	76.7899	81	1391	95	below_threshold
Rossellomorea arthrocnemi	strain=EAR8	GCA_904424705.1	2769542	2769542	type	True	76.5799	88	1391	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	76.5548	61	1391	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.5093	79	1391	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	76.5043	65	1391	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	76.2983	52	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:56,072] [INFO] DFAST Taxonomy check result was written to GCF_016908565.1_ASM1690856v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:56,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:56,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:56,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/checkm_data
[2024-01-24 15:18:56,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:56,120] [INFO] Task started: CheckM
[2024-01-24 15:18:56,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908565.1_ASM1690856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908565.1_ASM1690856v1_genomic.fna/checkm_input GCF_016908565.1_ASM1690856v1_genomic.fna/checkm_result
[2024-01-24 15:19:34,747] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:34,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,767] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:34,768] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:34,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908565.1_ASM1690856v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:34,769] [INFO] Task started: Blastn
[2024-01-24 15:19:34,769] [INFO] Running command: blastn -query GCF_016908565.1_ASM1690856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ae0e0c-6c1c-450c-ac72-a9a695935606/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908565.1_ASM1690856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:35,600] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:35,604] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:35,605] [INFO] Target genome list was writen to GCF_016908565.1_ASM1690856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:35,614] [INFO] Task started: fastANI
[2024-01-24 15:19:35,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg5400c574-0842-497b-9ae2-f4594527ec95/GCF_016908565.1_ASM1690856v1_genomic.fna.gz --refList GCF_016908565.1_ASM1690856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908565.1_ASM1690856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:45,782] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:45,795] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:45,795] [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_016908565.1	s__Sutcliffiella_A tianshenii	100.0	1390	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002157855.1	s__Sutcliffiella_A horikoshii_C	79.8063	452	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	96.53	95.82	0.92	0.90	4	-
GCF_002019665.1	s__Sutcliffiella_A halmapala	79.8	496	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001636495.1	s__Sutcliffiella_A horikoshii_A	79.5967	466	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180725.1	s__Sutcliffiella_A horikoshii_B	79.5641	445	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524115.1	s__Sutcliffiella_A sp012524115	79.5587	427	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911845.1	s__Sutcliffiella_A sp012911845	79.494	442	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001648575.1	s__Sutcliffiella_A horikoshii	79.451	456	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	76.866	88	1391	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_002551815.1	s__Bacillus_A sp002551815	76.433	55	1391	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:45,796] [INFO] GTDB search result was written to GCF_016908565.1_ASM1690856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:45,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:45,800] [INFO] DFAST_QC result json was written to GCF_016908565.1_ASM1690856v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:45,801] [INFO] DFAST_QC completed!
[2024-01-24 15:19:45,801] [INFO] Total running time: 0h1m19s