[2024-01-25 19:56:05,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference
[2024-01-25 19:56:06,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,726] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf84b7f4-3836-4390-b5a8-017e64df7047/GCF_003515685.1_ASM351568v1_genomic.fna.gz | prodigal -d GCF_003515685.1_ASM351568v1_genomic.fna/cds.fna -a GCF_003515685.1_ASM351568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:17,032] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:17,032] [INFO] Task started: HMMsearch
[2024-01-25 19:56:17,032] [INFO] Running command: hmmsearch --tblout GCF_003515685.1_ASM351568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/reference_markers.hmm GCF_003515685.1_ASM351568v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:17,418] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:17,432] [INFO] Found 6/6 markers.
[2024-01-25 19:56:17,478] [INFO] Query marker FASTA was written to GCF_003515685.1_ASM351568v1_genomic.fna/markers.fasta
[2024-01-25 19:56:17,479] [INFO] Task started: Blastn
[2024-01-25 19:56:17,479] [INFO] Running command: blastn -query GCF_003515685.1_ASM351568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/reference_markers.fasta -out GCF_003515685.1_ASM351568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:18,047] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:18,050] [INFO] Selected 22 target genomes.
[2024-01-25 19:56:18,050] [INFO] Target genome list was writen to GCF_003515685.1_ASM351568v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:18,073] [INFO] Task started: fastANI
[2024-01-25 19:56:18,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf84b7f4-3836-4390-b5a8-017e64df7047/GCF_003515685.1_ASM351568v1_genomic.fna.gz --refList GCF_003515685.1_ASM351568v1_genomic.fna/target_genomes.txt --output GCF_003515685.1_ASM351568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:38,595] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:38,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:38,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:38,615] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:38,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:38,616] [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
Neobacillus notoginsengisoli	strain=JCM 30743	GCA_003515685.1	1578198	1578198	type	True	100.0	1563	1565	95	conclusive
Neobacillus piezotolerans	strain=YLB-04	GCA_003362805.1	2259171	2259171	type	True	79.173	485	1565	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.7357	164	1565	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	77.5515	130	1565	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	77.309	129	1565	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	77.3062	97	1565	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	77.2436	79	1565	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.2336	100	1565	95	below_threshold
Bacillus testis	strain=SIT10	GCA_001243895.1	1622072	1622072	type	True	77.2198	52	1565	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.18	115	1565	95	below_threshold
Mesobacillus selenatarsenatis	strain=SF-1	GCA_000813125.1	388741	388741	type	True	77.0725	120	1565	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	76.9469	152	1565	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	76.8555	109	1565	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_001456935.1	1402860	1402860	type	True	76.818	53	1565	95	below_threshold
Falsibacillus pallidus	strain=DSM 25281	GCA_003350505.1	493781	493781	type	True	76.7508	60	1565	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	76.7494	139	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:38,624] [INFO] DFAST Taxonomy check result was written to GCF_003515685.1_ASM351568v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:38,626] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:38,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:38,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/checkm_data
[2024-01-25 19:56:38,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:38,683] [INFO] Task started: CheckM
[2024-01-25 19:56:38,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003515685.1_ASM351568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003515685.1_ASM351568v1_genomic.fna/checkm_input GCF_003515685.1_ASM351568v1_genomic.fna/checkm_result
[2024-01-25 19:57:11,870] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:11,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:11,892] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:11,892] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:11,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003515685.1_ASM351568v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:11,893] [INFO] Task started: Blastn
[2024-01-25 19:57:11,893] [INFO] Running command: blastn -query GCF_003515685.1_ASM351568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb3a0e1b-be08-4350-9807-8b6b056ba1d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003515685.1_ASM351568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:12,659] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:12,662] [INFO] Selected 21 target genomes.
[2024-01-25 19:57:12,662] [INFO] Target genome list was writen to GCF_003515685.1_ASM351568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:12,682] [INFO] Task started: fastANI
[2024-01-25 19:57:12,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf84b7f4-3836-4390-b5a8-017e64df7047/GCF_003515685.1_ASM351568v1_genomic.fna.gz --refList GCF_003515685.1_ASM351568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003515685.1_ASM351568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:31,287] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:31,297] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:31,298] [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_003515685.1	s__Bacillus_D notoginsengisoli	100.0	1563	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000821085.1	s__Bacillus_D sp000821085	81.0539	858	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003362805.1	s__Bacillus_D piezotolerans	79.1746	485	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273955.1	s__Bacillus_D sp001273955	79.1383	530	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001510665.1	s__Bacillus_D sp001510665	79.0475	550	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685025.1	s__Bacillus_D sp001685025	78.5989	374	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278805.1	s__Bacillus_D sp001278805	78.3649	348	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613125.1	s__Bacillus_D sp000613125	78.3507	353	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613155.1	s__Mesobacillus sp018613155	77.2917	115	1565	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	77.1801	109	1565	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_001274725.1	s__Cytobacillus globisporus	77.1472	119	1565	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_000759675.1	s__Neobacillus niacini_A	77.1314	133	1565	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_019039215.1	s__Cytobacillus sp019039215	77.0671	100	1565	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_017303275.1	s__Cytobacillus sp017303275	77.0467	119	1565	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_002272245.1	s__Neobacillus sp002272245	76.752	104	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.06	97.06	0.86	0.86	2	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	76.5849	62	1565	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:31,301] [INFO] GTDB search result was written to GCF_003515685.1_ASM351568v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:31,302] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:31,305] [INFO] DFAST_QC result json was written to GCF_003515685.1_ASM351568v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:31,305] [INFO] DFAST_QC completed!
[2024-01-25 19:57:31,305] [INFO] Total running time: 0h1m26s