[2024-01-25 19:35:05,664] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,666] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference
[2024-01-25 19:35:06,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,841] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,841] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9c92178-1d5c-409e-b6ca-8850afe995a9/GCF_030814065.1_ASM3081406v1_genomic.fna.gz | prodigal -d GCF_030814065.1_ASM3081406v1_genomic.fna/cds.fna -a GCF_030814065.1_ASM3081406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:15,112] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:15,112] [INFO] Task started: HMMsearch
[2024-01-25 19:35:15,112] [INFO] Running command: hmmsearch --tblout GCF_030814065.1_ASM3081406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/reference_markers.hmm GCF_030814065.1_ASM3081406v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:15,358] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:15,359] [INFO] Found 6/6 markers.
[2024-01-25 19:35:15,389] [INFO] Query marker FASTA was written to GCF_030814065.1_ASM3081406v1_genomic.fna/markers.fasta
[2024-01-25 19:35:15,390] [INFO] Task started: Blastn
[2024-01-25 19:35:15,390] [INFO] Running command: blastn -query GCF_030814065.1_ASM3081406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/reference_markers.fasta -out GCF_030814065.1_ASM3081406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:15,946] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:15,949] [INFO] Selected 16 target genomes.
[2024-01-25 19:35:15,949] [INFO] Target genome list was writen to GCF_030814065.1_ASM3081406v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:15,954] [INFO] Task started: fastANI
[2024-01-25 19:35:15,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c92178-1d5c-409e-b6ca-8850afe995a9/GCF_030814065.1_ASM3081406v1_genomic.fna.gz --refList GCF_030814065.1_ASM3081406v1_genomic.fna/target_genomes.txt --output GCF_030814065.1_ASM3081406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:27,149] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:27,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:27,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:27,158] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:35:27,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:35:27,158] [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
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	80.6521	621	1279	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_000517385.1	308892	308892	type	True	80.4635	583	1279	95	below_threshold
Mesobacillus jeotgali	strain=DSM 18226	GCA_002874535.1	129985	129985	type	True	80.4491	641	1279	95	below_threshold
Mesobacillus boroniphilus	strain=JCM 21738	GCA_001315165.1	308892	308892	type	True	80.4293	586	1279	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	79.9227	521	1279	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	77.3084	145	1279	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_013618945.1	1917180	1917180	type	True	77.2188	153	1279	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	77.2062	152	1279	95	below_threshold
Neobacillus piezotolerans	strain=YLB-04	GCA_003362805.1	2259171	2259171	type	True	76.8832	87	1279	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	76.7204	114	1279	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	76.6918	113	1279	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	76.6561	115	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:27,160] [INFO] DFAST Taxonomy check result was written to GCF_030814065.1_ASM3081406v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:27,163] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:27,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:27,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/checkm_data
[2024-01-25 19:35:27,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:27,203] [INFO] Task started: CheckM
[2024-01-25 19:35:27,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814065.1_ASM3081406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814065.1_ASM3081406v1_genomic.fna/checkm_input GCF_030814065.1_ASM3081406v1_genomic.fna/checkm_result
[2024-01-25 19:35:55,723] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:55,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:55,743] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:55,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:55,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814065.1_ASM3081406v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:55,744] [INFO] Task started: Blastn
[2024-01-25 19:35:55,744] [INFO] Running command: blastn -query GCF_030814065.1_ASM3081406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6508679-0a95-4d86-8c90-2cada73f0350/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814065.1_ASM3081406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:56,519] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:56,523] [INFO] Selected 11 target genomes.
[2024-01-25 19:35:56,523] [INFO] Target genome list was writen to GCF_030814065.1_ASM3081406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:56,532] [INFO] Task started: fastANI
[2024-01-25 19:35:56,532] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c92178-1d5c-409e-b6ca-8850afe995a9/GCF_030814065.1_ASM3081406v1_genomic.fna.gz --refList GCF_030814065.1_ASM3081406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814065.1_ASM3081406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:07,458] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:07,466] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:07,466] [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_000934845.1	s__Mesobacillus subterraneus_A	99.1208	1089	1279	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	conclusive
GCF_018613055.1	s__Mesobacillus sp018613055	84.3548	857	1279	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007678455.1	s__Mesobacillus oceanisediminis_A	83.8557	831	1279	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_900166585.1	s__Mesobacillus jeotgali_A	81.4647	714	1279	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_014856545.1	s__Mesobacillus sp014856545	80.9052	637	1279	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_018613235.1	s__Mesobacillus sp018613235	80.75	640	1279	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_018613155.1	s__Mesobacillus sp018613155	80.5446	618	1279	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_012163115.1	s__Mesobacillus selenatarsenatis_A	80.5412	626	1279	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_018613315.1	s__Mesobacillus sp018613315	80.5136	625	1279	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_002874535.1	s__Mesobacillus jeotgali	80.4631	639	1279	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_018424685.1	s__Mesobacillus boroniphilus_A	80.2012	639	1279	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:07,469] [INFO] GTDB search result was written to GCF_030814065.1_ASM3081406v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:07,469] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:07,472] [INFO] DFAST_QC result json was written to GCF_030814065.1_ASM3081406v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:07,472] [INFO] DFAST_QC completed!
[2024-01-25 19:36:07,472] [INFO] Total running time: 0h1m2s