[2024-01-25 18:16:50,886] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:50,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:50,890] [INFO] DQC Reference Directory: /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference
[2024-01-25 18:16:52,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:52,046] [INFO] Task started: Prodigal
[2024-01-25 18:16:52,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgca1b2589-1eb1-41ff-9ad0-a83bb8016f22/GCF_018101145.1_ASM1810114v1_genomic.fna.gz | prodigal -d GCF_018101145.1_ASM1810114v1_genomic.fna/cds.fna -a GCF_018101145.1_ASM1810114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:00,732] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:00,733] [INFO] Task started: HMMsearch
[2024-01-25 18:17:00,733] [INFO] Running command: hmmsearch --tblout GCF_018101145.1_ASM1810114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/reference_markers.hmm GCF_018101145.1_ASM1810114v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:00,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:00,952] [INFO] Found 6/6 markers.
[2024-01-25 18:17:00,979] [INFO] Query marker FASTA was written to GCF_018101145.1_ASM1810114v1_genomic.fna/markers.fasta
[2024-01-25 18:17:00,980] [INFO] Task started: Blastn
[2024-01-25 18:17:00,980] [INFO] Running command: blastn -query GCF_018101145.1_ASM1810114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/reference_markers.fasta -out GCF_018101145.1_ASM1810114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:01,536] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:01,539] [INFO] Selected 15 target genomes.
[2024-01-25 18:17:01,540] [INFO] Target genome list was writen to GCF_018101145.1_ASM1810114v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:01,545] [INFO] Task started: fastANI
[2024-01-25 18:17:01,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1b2589-1eb1-41ff-9ad0-a83bb8016f22/GCF_018101145.1_ASM1810114v1_genomic.fna.gz --refList GCF_018101145.1_ASM1810114v1_genomic.fna/target_genomes.txt --output GCF_018101145.1_ASM1810114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:12,584] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:12,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:12,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:12,591] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:17:12,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:17:12,591] [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
Weizmannia coagulans	strain=DSM 1	GCA_900128875.1	1398	1398	suspected-type	True	94.7192	843	1152	95	below_threshold
Weizmannia coagulans	strain=ATCC 7050	GCA_000420205.1	1398	1398	suspected-type	True	94.6948	831	1152	95	below_threshold
Weizmannia coagulans	strain=DSM 1	GCA_000290615.1	1398	1398	suspected-type	True	94.6694	840	1152	95	below_threshold
Weizmannia coagulans	strain=ATCC 7050	GCA_000832905.1	1398	1398	suspected-type	True	94.5577	919	1152	95	below_threshold
Weizmannia acidiproducens	strain=DSM 23148	GCA_000374345.1	1121084	1121084	type	True	78.8406	454	1152	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	78.8276	65	1152	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.5305	61	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:12,593] [INFO] DFAST Taxonomy check result was written to GCF_018101145.1_ASM1810114v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:12,593] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:12,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:12,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/checkm_data
[2024-01-25 18:17:12,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:12,630] [INFO] Task started: CheckM
[2024-01-25 18:17:12,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018101145.1_ASM1810114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018101145.1_ASM1810114v1_genomic.fna/checkm_input GCF_018101145.1_ASM1810114v1_genomic.fna/checkm_result
[2024-01-25 18:17:42,052] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:42,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:42,095] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:42,095] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:42,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018101145.1_ASM1810114v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:42,096] [INFO] Task started: Blastn
[2024-01-25 18:17:42,096] [INFO] Running command: blastn -query GCF_018101145.1_ASM1810114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge97311bd-e848-40ae-817f-ef49f1c2960f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018101145.1_ASM1810114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:42,903] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:42,907] [INFO] Selected 20 target genomes.
[2024-01-25 18:17:42,907] [INFO] Target genome list was writen to GCF_018101145.1_ASM1810114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:42,941] [INFO] Task started: fastANI
[2024-01-25 18:17:42,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgca1b2589-1eb1-41ff-9ad0-a83bb8016f22/GCF_018101145.1_ASM1810114v1_genomic.fna.gz --refList GCF_018101145.1_ASM1810114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018101145.1_ASM1810114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:57,758] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:57,765] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:57,765] [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_000169195.2	s__Weizmannia coagulans_A	98.2146	1039	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	98.29	97.76	0.92	0.89	29	conclusive
GCF_000290615.1	s__Weizmannia coagulans	94.6906	839	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	98.84	97.70	0.92	0.87	18	-
GCF_008974185.1	s__Weizmannia sp008974185	80.4482	647	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.76	99.74	0.95	0.95	3	-
GCF_000751775.1	s__Bacillus_J thermoamylovorans	79.0732	73	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	98.31	97.86	0.86	0.85	9	-
GCF_000374345.1	s__Weizmannia acidiproducens	78.8542	452	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001610955.1	s__Geobacillus thermoleovorans	78.4936	73	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	-
GCF_000011645.1	s__Bacillus licheniformis	78.3105	66	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_000986785.1	s__Bacillus_AZ campisalis	77.4161	50	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001461825.1	s__Bacillus velezensis	76.3858	55	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
GCF_002860205.1	s__T33-2 sp002860205	76.3735	51	1152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__T33-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:57,766] [INFO] GTDB search result was written to GCF_018101145.1_ASM1810114v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:57,767] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:57,769] [INFO] DFAST_QC result json was written to GCF_018101145.1_ASM1810114v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:57,769] [INFO] DFAST_QC completed!
[2024-01-25 18:17:57,769] [INFO] Total running time: 0h1m7s