[2024-01-24 13:49:29,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,905] [INFO] DQC Reference Directory: /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference
[2024-01-24 13:49:31,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:31,336] [INFO] Task started: Prodigal
[2024-01-24 13:49:31,336] [INFO] Running command: gunzip -c /var/lib/cwl/stgcacd01d7-e106-4893-826b-477772f66e3f/GCF_003049615.1_ASM304961v1_genomic.fna.gz | prodigal -d GCF_003049615.1_ASM304961v1_genomic.fna/cds.fna -a GCF_003049615.1_ASM304961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:39,723] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:39,724] [INFO] Task started: HMMsearch
[2024-01-24 13:49:39,724] [INFO] Running command: hmmsearch --tblout GCF_003049615.1_ASM304961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/reference_markers.hmm GCF_003049615.1_ASM304961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:40,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:40,116] [INFO] Found 6/6 markers.
[2024-01-24 13:49:40,155] [INFO] Query marker FASTA was written to GCF_003049615.1_ASM304961v1_genomic.fna/markers.fasta
[2024-01-24 13:49:40,155] [INFO] Task started: Blastn
[2024-01-24 13:49:40,155] [INFO] Running command: blastn -query GCF_003049615.1_ASM304961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/reference_markers.fasta -out GCF_003049615.1_ASM304961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,850] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,853] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:40,854] [INFO] Target genome list was writen to GCF_003049615.1_ASM304961v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:40,858] [INFO] Task started: fastANI
[2024-01-24 13:49:40,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacd01d7-e106-4893-826b-477772f66e3f/GCF_003049615.1_ASM304961v1_genomic.fna.gz --refList GCF_003049615.1_ASM304961v1_genomic.fna/target_genomes.txt --output GCF_003049615.1_ASM304961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,164] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,176] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:49,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:49,176] [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
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	100.0	1353	1356	95	conclusive
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	99.9725	1217	1356	95	conclusive
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	81.9402	664	1356	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	81.9402	664	1356	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.5401	337	1356	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	78.7675	367	1356	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	78.7674	369	1356	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	78.0061	207	1356	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.5764	161	1356	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	77.5456	81	1356	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.1303	50	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,178] [INFO] DFAST Taxonomy check result was written to GCF_003049615.1_ASM304961v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/checkm_data
[2024-01-24 13:49:49,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,224] [INFO] Task started: CheckM
[2024-01-24 13:49:49,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049615.1_ASM304961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049615.1_ASM304961v1_genomic.fna/checkm_input GCF_003049615.1_ASM304961v1_genomic.fna/checkm_result
[2024-01-24 13:50:21,129] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:21,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,154] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:21,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:21,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049615.1_ASM304961v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:21,156] [INFO] Task started: Blastn
[2024-01-24 13:50:21,156] [INFO] Running command: blastn -query GCF_003049615.1_ASM304961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf89a7217-f8a6-4d9a-b79a-db2b2fdb1218/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049615.1_ASM304961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:21,943] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:21,947] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:21,948] [INFO] Target genome list was writen to GCF_003049615.1_ASM304961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:21,957] [INFO] Task started: fastANI
[2024-01-24 13:50:21,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacd01d7-e106-4893-826b-477772f66e3f/GCF_003049615.1_ASM304961v1_genomic.fna.gz --refList GCF_003049615.1_ASM304961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049615.1_ASM304961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:30,679] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:30,695] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:30,695] [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_003217295.1	s__Ureibacillus chungkukjangi	99.9725	1217	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_005491425.1	s__Ureibacillus sp005491425	84.2393	893	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772955.1	s__Ureibacillus sinduriensis	81.9402	664	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836845.1	s__Ureibacillus sp014836845	80.0162	508	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	80.012	493	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966145.1	s__Ureibacillus telephonicus	79.5281	462	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628435.1	s__Ureibacillus endophyticus	79.4459	385	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515775.1	s__Ureibacillus yapensis	79.4365	427	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908465.1	s__Ureibacillus composti	78.7442	369	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836905.1	s__Solibacillus sp014836905	78.0585	197	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.631	160	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,696] [INFO] GTDB search result was written to GCF_003049615.1_ASM304961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:30,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:30,703] [INFO] DFAST_QC result json was written to GCF_003049615.1_ASM304961v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:30,704] [INFO] DFAST_QC completed!
[2024-01-24 13:50:30,704] [INFO] Total running time: 0h1m1s