[2024-01-24 13:01:23,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:23,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:23,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference
[2024-01-24 13:01:25,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,372] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,372] [INFO] Running command: gunzip -c /var/lib/cwl/stg35149413-1a9f-46fb-bf92-761253942b8f/GCF_003049565.1_ASM304956v1_genomic.fna.gz | prodigal -d GCF_003049565.1_ASM304956v1_genomic.fna/cds.fna -a GCF_003049565.1_ASM304956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:34,785] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:34,786] [INFO] Task started: HMMsearch
[2024-01-24 13:01:34,786] [INFO] Running command: hmmsearch --tblout GCF_003049565.1_ASM304956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/reference_markers.hmm GCF_003049565.1_ASM304956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:35,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:35,081] [INFO] Found 6/6 markers.
[2024-01-24 13:01:35,124] [INFO] Query marker FASTA was written to GCF_003049565.1_ASM304956v1_genomic.fna/markers.fasta
[2024-01-24 13:01:35,124] [INFO] Task started: Blastn
[2024-01-24 13:01:35,124] [INFO] Running command: blastn -query GCF_003049565.1_ASM304956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/reference_markers.fasta -out GCF_003049565.1_ASM304956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:35,723] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:35,727] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:35,727] [INFO] Target genome list was writen to GCF_003049565.1_ASM304956v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:35,733] [INFO] Task started: fastANI
[2024-01-24 13:01:35,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg35149413-1a9f-46fb-bf92-761253942b8f/GCF_003049565.1_ASM304956v1_genomic.fna.gz --refList GCF_003049565.1_ASM304956v1_genomic.fna/target_genomes.txt --output GCF_003049565.1_ASM304956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:46,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:46,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:46,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:46,590] [INFO] Found 10 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:01:46,590] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:01:46,591] [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
Lysinibacillus tabacifolii	strain=K3514	GCA_003049565.1	1173107	1173107	suspected-type	True	100.0	1492	1493	95	inconclusive
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	99.9986	1486	1493	95	inconclusive
Lysinibacillus sphaericus	strain=NRRL B-23268	GCA_005217555.1	1421	1421	suspected-type	True	99.0865	1356	1493	95	inconclusive
Lysinibacillus sphaericus	strain=NCTC10338	GCA_900445465.1	1421	1421	suspected-type	True	99.0315	1396	1493	95	inconclusive
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	99.0219	1358	1493	95	inconclusive
Lysinibacillus sphaericus	strain=NBRC 15095	GCA_006539805.1	1421	1421	suspected-type	True	99.0174	1348	1493	95	inconclusive
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	98.9857	1390	1493	95	inconclusive
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	81.683	740	1493	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	80.3675	599	1493	95	below_threshold
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	77.8155	93	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:46,592] [INFO] DFAST Taxonomy check result was written to GCF_003049565.1_ASM304956v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:46,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:46,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:46,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/checkm_data
[2024-01-24 13:01:46,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:46,641] [INFO] Task started: CheckM
[2024-01-24 13:01:46,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049565.1_ASM304956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049565.1_ASM304956v1_genomic.fna/checkm_input GCF_003049565.1_ASM304956v1_genomic.fna/checkm_result
[2024-01-24 13:02:19,383] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:19,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:19,406] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:19,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:19,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049565.1_ASM304956v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:19,408] [INFO] Task started: Blastn
[2024-01-24 13:02:19,408] [INFO] Running command: blastn -query GCF_003049565.1_ASM304956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89014c01-2f1a-4ca6-af0a-4e8e16eece2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049565.1_ASM304956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:20,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:20,236] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:20,236] [INFO] Target genome list was writen to GCF_003049565.1_ASM304956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:20,246] [INFO] Task started: fastANI
[2024-01-24 13:02:20,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg35149413-1a9f-46fb-bf92-761253942b8f/GCF_003049565.1_ASM304956v1_genomic.fna.gz --refList GCF_003049565.1_ASM304956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049565.1_ASM304956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:31,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:31,202] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:02:31,202] [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_002982115.1	s__Lysinibacillus sphaericus	99.0274	1399	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.42	98.91	0.95	0.90	10	inconclusive
GCF_003049665.1	s__Lysinibacillus mangiferihumi	96.9335	1312	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	inconclusive
GCF_001728805.1	s__Lysinibacillus sphaericus_D	96.102	1315	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.1498	99.28	99.28	0.92	0.92	2	-
GCA_015999545.1	s__Lysinibacillus sp002340205	86.4606	1162	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.79	97.71	0.94	0.94	5	-
GCF_000392615.1	s__Lysinibacillus sphaericus_B	82.5751	861	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007362955.1	s__Lysinibacillus fusiformis_E	82.461	885	1493	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_001708185.1	s__Lysinibacillus xylanilyticus_A	82.2421	800	1493	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_002237755.1	s__Lysinibacillus sp002237755	81.942	779	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
GCF_001275675.1	s__Lysinibacillus sp001275675	81.9094	826	1493	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:31,204] [INFO] GTDB search result was written to GCF_003049565.1_ASM304956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:31,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:31,209] [INFO] DFAST_QC result json was written to GCF_003049565.1_ASM304956v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:31,210] [INFO] DFAST_QC completed!
[2024-01-24 13:02:31,210] [INFO] Total running time: 0h1m7s