[2024-01-25 19:48:05,531] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference
[2024-01-25 19:48:06,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,687] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,688] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc1851b6-c2f5-404e-8131-208687da3ced/GCF_028735875.1_ASM2873587v1_genomic.fna.gz | prodigal -d GCF_028735875.1_ASM2873587v1_genomic.fna/cds.fna -a GCF_028735875.1_ASM2873587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:14,677] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:14,677] [INFO] Task started: HMMsearch
[2024-01-25 19:48:14,677] [INFO] Running command: hmmsearch --tblout GCF_028735875.1_ASM2873587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/reference_markers.hmm GCF_028735875.1_ASM2873587v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:14,919] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:14,920] [INFO] Found 6/6 markers.
[2024-01-25 19:48:14,951] [INFO] Query marker FASTA was written to GCF_028735875.1_ASM2873587v1_genomic.fna/markers.fasta
[2024-01-25 19:48:14,952] [INFO] Task started: Blastn
[2024-01-25 19:48:14,952] [INFO] Running command: blastn -query GCF_028735875.1_ASM2873587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/reference_markers.fasta -out GCF_028735875.1_ASM2873587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:15,493] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:15,498] [INFO] Selected 32 target genomes.
[2024-01-25 19:48:15,498] [INFO] Target genome list was writen to GCF_028735875.1_ASM2873587v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:15,514] [INFO] Task started: fastANI
[2024-01-25 19:48:15,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc1851b6-c2f5-404e-8131-208687da3ced/GCF_028735875.1_ASM2873587v1_genomic.fna.gz --refList GCF_028735875.1_ASM2873587v1_genomic.fna/target_genomes.txt --output GCF_028735875.1_ASM2873587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:37,428] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:37,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:37,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:37,438] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:48:37,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:48:37,439] [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
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	80.258	75	1354	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	79.5491	68	1354	95	below_threshold
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	79.5468	71	1354	95	below_threshold
Bacillus cytotoxicus	strain=NVH 391-98	GCA_000017425.1	580165	580165	type	True	79.0611	60	1354	95	below_threshold
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.5978	260	1354	95	below_threshold
Alkalihalobacillus xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	78.5111	286	1354	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.572	65	1354	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.5058	70	1354	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.5047	70	1354	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.3374	85	1354	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.6297	79	1354	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.5771	86	1354	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.5077	85	1354	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.3832	67	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:37,440] [INFO] DFAST Taxonomy check result was written to GCF_028735875.1_ASM2873587v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:37,441] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:37,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:37,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/checkm_data
[2024-01-25 19:48:37,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:37,484] [INFO] Task started: CheckM
[2024-01-25 19:48:37,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028735875.1_ASM2873587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028735875.1_ASM2873587v1_genomic.fna/checkm_input GCF_028735875.1_ASM2873587v1_genomic.fna/checkm_result
[2024-01-25 19:49:06,088] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:06,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:06,110] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:06,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:06,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028735875.1_ASM2873587v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:06,110] [INFO] Task started: Blastn
[2024-01-25 19:49:06,110] [INFO] Running command: blastn -query GCF_028735875.1_ASM2873587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9a1e366-880f-4734-bffd-78348b75ce33/dqc_reference/reference_markers_gtdb.fasta -out GCF_028735875.1_ASM2873587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:06,886] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:06,889] [INFO] Selected 19 target genomes.
[2024-01-25 19:49:06,890] [INFO] Target genome list was writen to GCF_028735875.1_ASM2873587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:06,916] [INFO] Task started: fastANI
[2024-01-25 19:49:06,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc1851b6-c2f5-404e-8131-208687da3ced/GCF_028735875.1_ASM2873587v1_genomic.fna.gz --refList GCF_028735875.1_ASM2873587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028735875.1_ASM2873587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:22,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:22,783] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:22,783] [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_007725405.1	s__Bacillus_H miscanthi	99.0465	1261	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	conclusive
GCF_002019765.1	s__Bacillus_H oshimensis	91.0454	1227	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	-
GCF_900177675.1	s__Neobacillus sp900177675	80.3902	55	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	80.3703	76	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900197585.1	s__Bacillus_H sp900197585	80.3204	604	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002276165.1	s__Cytobacillus kochii	79.7364	53	1354	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_001866075.3	s__Anaerobacillus isosaccharinicus	79.1981	66	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	78.8861	88	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002019705.1	s__Bacillus_H patagoniensis	78.6799	262	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907895.1	s__Bacillus_H xiaoxiensis	78.482	288	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCF_001598215.1	s__Bacillus_H clausii_B	77.8126	123	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.35	99.35	0.94	0.94	2	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.3383	85	1354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:22,785] [INFO] GTDB search result was written to GCF_028735875.1_ASM2873587v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:22,790] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:22,793] [INFO] DFAST_QC result json was written to GCF_028735875.1_ASM2873587v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:22,794] [INFO] DFAST_QC completed!
[2024-01-25 19:49:22,794] [INFO] Total running time: 0h1m17s