[2024-01-25 18:54:20,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,466] [INFO] DQC Reference Directory: /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference
[2024-01-25 18:54:21,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,613] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgab62e29f-7a3c-4fcd-9869-86aea90abeef/GCF_003049645.1_ASM304964v1_genomic.fna.gz | prodigal -d GCF_003049645.1_ASM304964v1_genomic.fna/cds.fna -a GCF_003049645.1_ASM304964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:28,344] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:28,344] [INFO] Task started: HMMsearch
[2024-01-25 18:54:28,344] [INFO] Running command: hmmsearch --tblout GCF_003049645.1_ASM304964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/reference_markers.hmm GCF_003049645.1_ASM304964v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:28,576] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:28,577] [INFO] Found 6/6 markers.
[2024-01-25 18:54:28,605] [INFO] Query marker FASTA was written to GCF_003049645.1_ASM304964v1_genomic.fna/markers.fasta
[2024-01-25 18:54:28,606] [INFO] Task started: Blastn
[2024-01-25 18:54:28,606] [INFO] Running command: blastn -query GCF_003049645.1_ASM304964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/reference_markers.fasta -out GCF_003049645.1_ASM304964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:29,157] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:29,161] [INFO] Selected 26 target genomes.
[2024-01-25 18:54:29,161] [INFO] Target genome list was writen to GCF_003049645.1_ASM304964v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:29,190] [INFO] Task started: fastANI
[2024-01-25 18:54:29,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgab62e29f-7a3c-4fcd-9869-86aea90abeef/GCF_003049645.1_ASM304964v1_genomic.fna.gz --refList GCF_003049645.1_ASM304964v1_genomic.fna/target_genomes.txt --output GCF_003049645.1_ASM304964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:46,134] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:46,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:46,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:46,148] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:46,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:46,148] [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
Lysinibacillus agricola	strain=FJAT-51161	GCA_016638705.1	2590012	2590012	type	True	78.3222	221	1189	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	78.3212	209	1189	95	below_threshold
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	78.3162	204	1189	95	below_threshold
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	78.2824	197	1189	95	below_threshold
Lysinibacillus tabacifolii	strain=K3514	GCA_003049565.1	1173107	1173107	suspected-type	True	78.2561	208	1189	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	78.1884	241	1189	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	78.1564	227	1189	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	78.1427	232	1189	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	78.1141	209	1189	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.1034	239	1189	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	78.0767	271	1189	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	77.984	179	1189	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	77.9285	237	1189	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.8763	185	1189	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.8584	181	1189	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_002200915.1	309788	309788	type	True	77.8266	229	1189	95	below_threshold
Lysinibacillus boronitolerans	strain=NBRC 103108	GCA_000772935.1	309788	309788	type	True	77.8266	229	1189	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	77.807	184	1189	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	77.6935	223	1189	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	77.3675	70	1189	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.3739	59	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:46,153] [INFO] DFAST Taxonomy check result was written to GCF_003049645.1_ASM304964v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:46,153] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:46,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:46,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/checkm_data
[2024-01-25 18:54:46,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:46,194] [INFO] Task started: CheckM
[2024-01-25 18:54:46,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049645.1_ASM304964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049645.1_ASM304964v1_genomic.fna/checkm_input GCF_003049645.1_ASM304964v1_genomic.fna/checkm_result
[2024-01-25 18:55:10,391] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:10,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:10,413] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:10,414] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:10,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049645.1_ASM304964v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:10,414] [INFO] Task started: Blastn
[2024-01-25 18:55:10,414] [INFO] Running command: blastn -query GCF_003049645.1_ASM304964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc71c5450-4374-4af4-bafe-20d757dee2e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049645.1_ASM304964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:11,153] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:11,156] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:11,156] [INFO] Target genome list was writen to GCF_003049645.1_ASM304964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:11,170] [INFO] Task started: fastANI
[2024-01-25 18:55:11,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgab62e29f-7a3c-4fcd-9869-86aea90abeef/GCF_003049645.1_ASM304964v1_genomic.fna.gz --refList GCF_003049645.1_ASM304964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049645.1_ASM304964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:23,653] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:23,662] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:23,662] [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_003049645.1	s__Metasolibacillus fluoroglycofenilyticus	100.0	1189	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	98.96	98.96	0.94	0.94	2	conclusive
GCF_000612805.1	s__Metasolibacillus ndiopicus	84.2919	888	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049505.1	s__Metasolibacillus meyeri	83.2221	816	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982115.1	s__Lysinibacillus sphaericus	78.3293	203	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	-
GCF_016638705.1	s__Lysinibacillus sp001278875	78.3137	222	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.96	0.96	2	-
GCA_002360295.1	s__Metasolibacillus sp002360295	78.2708	268	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281525.1	s__Lysinibacillus macroides	78.0767	271	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_001728805.1	s__Lysinibacillus sphaericus_D	78.0411	224	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.1498	99.28	99.28	0.92	0.92	2	-
GCF_003628435.1	s__Ureibacillus endophyticus	78.0197	188	1189	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_006864135.1	s__Lysinibacillus sp006864135	77.9573	226	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	95.97	95.97	0.86	0.86	2	-
GCA_002973635.1	s__Lysinibacillus sp002973635	77.8177	230	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908465.1	s__Ureibacillus composti	77.804	185	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007362955.1	s__Lysinibacillus fusiformis_E	77.7678	225	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254155.1	s__Psychrobacillus insolitus	77.3675	70	1189	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:23,664] [INFO] GTDB search result was written to GCF_003049645.1_ASM304964v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:23,665] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:23,671] [INFO] DFAST_QC result json was written to GCF_003049645.1_ASM304964v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:23,671] [INFO] DFAST_QC completed!
[2024-01-25 18:55:23,671] [INFO] Total running time: 0h1m3s