[2024-01-25 18:11:20,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:20,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:20,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference
[2024-01-25 18:11:21,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:21,806] [INFO] Task started: Prodigal
[2024-01-25 18:11:21,807] [INFO] Running command: gunzip -c /var/lib/cwl/stgb19b3a17-d78c-4d3c-b6f0-625e06f04400/GCF_014836845.1_ASM1483684v1_genomic.fna.gz | prodigal -d GCF_014836845.1_ASM1483684v1_genomic.fna/cds.fna -a GCF_014836845.1_ASM1483684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:27,801] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:27,801] [INFO] Task started: HMMsearch
[2024-01-25 18:11:27,801] [INFO] Running command: hmmsearch --tblout GCF_014836845.1_ASM1483684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/reference_markers.hmm GCF_014836845.1_ASM1483684v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:28,028] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:28,029] [INFO] Found 6/6 markers.
[2024-01-25 18:11:28,060] [INFO] Query marker FASTA was written to GCF_014836845.1_ASM1483684v1_genomic.fna/markers.fasta
[2024-01-25 18:11:28,060] [INFO] Task started: Blastn
[2024-01-25 18:11:28,060] [INFO] Running command: blastn -query GCF_014836845.1_ASM1483684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/reference_markers.fasta -out GCF_014836845.1_ASM1483684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:28,627] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:28,631] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:28,631] [INFO] Target genome list was writen to GCF_014836845.1_ASM1483684v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:28,646] [INFO] Task started: fastANI
[2024-01-25 18:11:28,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19b3a17-d78c-4d3c-b6f0-625e06f04400/GCF_014836845.1_ASM1483684v1_genomic.fna.gz --refList GCF_014836845.1_ASM1483684v1_genomic.fna/target_genomes.txt --output GCF_014836845.1_ASM1483684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:39,610] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:39,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:39,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:39,619] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:39,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:39,619] [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=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.9514	518	1204	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.932	529	1204	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	79.4521	467	1204	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	79.4414	468	1204	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	79.1457	386	1204	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	79.1341	380	1204	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.9077	345	1204	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	78.9077	345	1204	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.4753	336	1204	95	below_threshold
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.312	213	1204	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	78.239	212	1204	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.5836	176	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:39,620] [INFO] DFAST Taxonomy check result was written to GCF_014836845.1_ASM1483684v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:39,621] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:39,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:39,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/checkm_data
[2024-01-25 18:11:39,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:39,661] [INFO] Task started: CheckM
[2024-01-25 18:11:39,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836845.1_ASM1483684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836845.1_ASM1483684v1_genomic.fna/checkm_input GCF_014836845.1_ASM1483684v1_genomic.fna/checkm_result
[2024-01-25 18:12:02,355] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:02,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:02,380] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:02,381] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:02,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836845.1_ASM1483684v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:02,381] [INFO] Task started: Blastn
[2024-01-25 18:12:02,381] [INFO] Running command: blastn -query GCF_014836845.1_ASM1483684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78018c88-e2d4-4e57-942a-cec4a46738fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836845.1_ASM1483684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:03,232] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:03,235] [INFO] Selected 14 target genomes.
[2024-01-25 18:12:03,236] [INFO] Target genome list was writen to GCF_014836845.1_ASM1483684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:03,263] [INFO] Task started: fastANI
[2024-01-25 18:12:03,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19b3a17-d78c-4d3c-b6f0-625e06f04400/GCF_014836845.1_ASM1483684v1_genomic.fna.gz --refList GCF_014836845.1_ASM1483684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836845.1_ASM1483684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:13,767] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:13,774] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:13,775] [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_014836845.1	s__Ureibacillus sp014836845	100.0	1202	1204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003711845.1	s__Ureibacillus halotolerans	90.5143	988	1204	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	80.5243	549	1204	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_005491425.1	s__Ureibacillus sp005491425	80.1729	560	1204	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_003217295.1	s__Ureibacillus chungkukjangi	79.9676	516	1204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003628435.1	s__Ureibacillus endophyticus	79.7035	457	1204	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	79.4519	467	1204	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_016908465.1	s__Ureibacillus composti	79.1385	381	1204	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_006864135.1	s__Lysinibacillus sp006864135	78.1065	217	1204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	95.97	95.97	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:13,776] [INFO] GTDB search result was written to GCF_014836845.1_ASM1483684v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:13,777] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:13,779] [INFO] DFAST_QC result json was written to GCF_014836845.1_ASM1483684v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:13,779] [INFO] DFAST_QC completed!
[2024-01-25 18:12:13,779] [INFO] Total running time: 0h0m53s