[2024-01-25 19:41:50,908] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:50,909] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:50,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference
[2024-01-25 19:41:52,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:52,107] [INFO] Task started: Prodigal
[2024-01-25 19:41:52,108] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc31322c-be35-4be6-b863-1feab6eb5bb1/GCF_001042485.2_ASM104248v2_genomic.fna.gz | prodigal -d GCF_001042485.2_ASM104248v2_genomic.fna/cds.fna -a GCF_001042485.2_ASM104248v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:04,358] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:04,359] [INFO] Task started: HMMsearch
[2024-01-25 19:42:04,359] [INFO] Running command: hmmsearch --tblout GCF_001042485.2_ASM104248v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/reference_markers.hmm GCF_001042485.2_ASM104248v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:04,696] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:04,698] [INFO] Found 6/6 markers.
[2024-01-25 19:42:04,737] [INFO] Query marker FASTA was written to GCF_001042485.2_ASM104248v2_genomic.fna/markers.fasta
[2024-01-25 19:42:04,738] [INFO] Task started: Blastn
[2024-01-25 19:42:04,738] [INFO] Running command: blastn -query GCF_001042485.2_ASM104248v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/reference_markers.fasta -out GCF_001042485.2_ASM104248v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:05,336] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:05,338] [INFO] Selected 10 target genomes.
[2024-01-25 19:42:05,339] [INFO] Target genome list was writen to GCF_001042485.2_ASM104248v2_genomic.fna/target_genomes.txt
[2024-01-25 19:42:05,345] [INFO] Task started: fastANI
[2024-01-25 19:42:05,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc31322c-be35-4be6-b863-1feab6eb5bb1/GCF_001042485.2_ASM104248v2_genomic.fna.gz --refList GCF_001042485.2_ASM104248v2_genomic.fna/target_genomes.txt --output GCF_001042485.2_ASM104248v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:14,672] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:14,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:14,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:14,681] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:42:14,681] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:42:14,681] [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
Bacillus licheniformis	strain=ATCC 14580	GCA_006094335.1	1402	1402	type	True	94.5368	1298	1489	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	94.5316	1304	1489	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_000008425.1	1402	1402	type	True	94.5139	1309	1489	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	94.4682	1330	1489	95	below_threshold
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	83.8752	1103	1489	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.6485	60	1489	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	77.5884	52	1489	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	77.4657	54	1489	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.3522	108	1489	95	below_threshold
Aeribacillus composti	strain=KCTC 33824	GCA_007827555.1	1868734	1868734	type	True	76.8407	66	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:14,682] [INFO] DFAST Taxonomy check result was written to GCF_001042485.2_ASM104248v2_genomic.fna/tc_result.tsv
[2024-01-25 19:42:14,683] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:14,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:14,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/checkm_data
[2024-01-25 19:42:14,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:14,725] [INFO] Task started: CheckM
[2024-01-25 19:42:14,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042485.2_ASM104248v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042485.2_ASM104248v2_genomic.fna/checkm_input GCF_001042485.2_ASM104248v2_genomic.fna/checkm_result
[2024-01-25 19:42:56,064] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:56,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:56,098] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:56,098] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:56,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042485.2_ASM104248v2_genomic.fna/markers.fasta)
[2024-01-25 19:42:56,099] [INFO] Task started: Blastn
[2024-01-25 19:42:56,099] [INFO] Running command: blastn -query GCF_001042485.2_ASM104248v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7771b2-e0f4-4fb9-bde8-2abd75893187/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042485.2_ASM104248v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:56,910] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:56,913] [INFO] Selected 8 target genomes.
[2024-01-25 19:42:56,913] [INFO] Target genome list was writen to GCF_001042485.2_ASM104248v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:56,919] [INFO] Task started: fastANI
[2024-01-25 19:42:56,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc31322c-be35-4be6-b863-1feab6eb5bb1/GCF_001042485.2_ASM104248v2_genomic.fna.gz --refList GCF_001042485.2_ASM104248v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001042485.2_ASM104248v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:05,808] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:05,815] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:05,815] [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_001042485.2	s__Bacillus paralicheniformis	100.0	1488	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0745	98.70	96.39	0.96	0.84	103	conclusive
GCF_001969855.1	s__Bacillus haynesii	95.026	1318	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_000011645.1	s__Bacillus licheniformis	94.5316	1304	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_001969815.1	s__Bacillus swezeyi	83.853	1108	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_900166645.1	s__Bacillus sonorensis_A	83.7056	1120	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.48	99.48	0.95	0.95	2	-
GCF_001592005.1	s__Bacillus sonorensis	82.8532	1026	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_002019595.1	s__Bacillus_BA abyssalis	77.2451	70	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_BA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827555.1	s__Aeribacillus composti	76.8765	65	1489	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Aeribacillaceae;g__Aeribacillus	95.0	98.74	98.37	0.88	0.77	10	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:05,816] [INFO] GTDB search result was written to GCF_001042485.2_ASM104248v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:05,817] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:05,819] [INFO] DFAST_QC result json was written to GCF_001042485.2_ASM104248v2_genomic.fna/dqc_result.json
[2024-01-25 19:43:05,820] [INFO] DFAST_QC completed!
[2024-01-25 19:43:05,820] [INFO] Total running time: 0h1m15s