[2024-01-24 15:02:24,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference
[2024-01-24 15:02:26,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,430] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg50e4f2e3-cfd1-4cf0-8891-0537ee9fb668/GCF_016638705.1_ASM1663870v1_genomic.fna.gz | prodigal -d GCF_016638705.1_ASM1663870v1_genomic.fna/cds.fna -a GCF_016638705.1_ASM1663870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:37,918] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:37,918] [INFO] Task started: HMMsearch
[2024-01-24 15:02:37,918] [INFO] Running command: hmmsearch --tblout GCF_016638705.1_ASM1663870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/reference_markers.hmm GCF_016638705.1_ASM1663870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:38,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:38,275] [INFO] Found 6/6 markers.
[2024-01-24 15:02:38,345] [INFO] Query marker FASTA was written to GCF_016638705.1_ASM1663870v1_genomic.fna/markers.fasta
[2024-01-24 15:02:38,345] [INFO] Task started: Blastn
[2024-01-24 15:02:38,346] [INFO] Running command: blastn -query GCF_016638705.1_ASM1663870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/reference_markers.fasta -out GCF_016638705.1_ASM1663870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:39,040] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:39,044] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:39,045] [INFO] Target genome list was writen to GCF_016638705.1_ASM1663870v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:39,078] [INFO] Task started: fastANI
[2024-01-24 15:02:39,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e4f2e3-cfd1-4cf0-8891-0537ee9fb668/GCF_016638705.1_ASM1663870v1_genomic.fna.gz --refList GCF_016638705.1_ASM1663870v1_genomic.fna/target_genomes.txt --output GCF_016638705.1_ASM1663870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:57,304] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:57,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:57,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:57,317] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:57,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:57,317] [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	100.0	1761	1761	95	conclusive
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	89.7891	1239	1761	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	82.5146	895	1761	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	82.2642	880	1761	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	82.2211	741	1761	95	below_threshold
Lysinibacillus tabacifolii	strain=K3514	GCA_003049565.1	1173107	1173107	suspected-type	True	82.1548	756	1761	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	82.0571	789	1761	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	82.0329	779	1761	95	below_threshold
Lysinibacillus macroides	strain=DSM 54	GCA_001281525.1	33935	33935	type	True	81.8725	754	1761	95	below_threshold
Lysinibacillus fusiformis	strain=NBRC 15717	GCA_006540205.1	28031	28031	type	True	81.831	857	1761	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	80.4216	553	1761	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.4097	113	1761	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	78.6427	56	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:57,319] [INFO] DFAST Taxonomy check result was written to GCF_016638705.1_ASM1663870v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:57,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:57,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:57,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/checkm_data
[2024-01-24 15:02:57,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:57,384] [INFO] Task started: CheckM
[2024-01-24 15:02:57,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016638705.1_ASM1663870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016638705.1_ASM1663870v1_genomic.fna/checkm_input GCF_016638705.1_ASM1663870v1_genomic.fna/checkm_result
[2024-01-24 15:03:36,558] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:36,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:36,586] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:36,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:36,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016638705.1_ASM1663870v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:36,587] [INFO] Task started: Blastn
[2024-01-24 15:03:36,588] [INFO] Running command: blastn -query GCF_016638705.1_ASM1663870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72dc566b-651e-49c9-a82d-144b324b0994/dqc_reference/reference_markers_gtdb.fasta -out GCF_016638705.1_ASM1663870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:37,577] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:37,580] [INFO] Selected 6 target genomes.
[2024-01-24 15:03:37,581] [INFO] Target genome list was writen to GCF_016638705.1_ASM1663870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:37,587] [INFO] Task started: fastANI
[2024-01-24 15:03:37,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg50e4f2e3-cfd1-4cf0-8891-0537ee9fb668/GCF_016638705.1_ASM1663870v1_genomic.fna.gz --refList GCF_016638705.1_ASM1663870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016638705.1_ASM1663870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:54,408] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:54,415] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:54,415] [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_016638705.1	s__Lysinibacillus sp001278875	100.0	1761	1761	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	99.95	99.95	0.96	0.96	2	conclusive
GCF_001275675.1	s__Lysinibacillus sp001275675	90.0773	1196	1761	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_001183605.1	s__Lysinibacillus xylanilyticus	89.7468	1242	1761	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	97.05	95.97	0.88	0.83	5	-
GCF_006864135.1	s__Lysinibacillus sp006864135	89.4106	1163	1761	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	95.97	95.97	0.86	0.86	2	-
GCF_002237755.1	s__Lysinibacillus sp002237755	89.1656	1226	1761	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_001708185.1	s__Lysinibacillus xylanilyticus_A	88.669	1122	1761	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 15:03:54,416] [INFO] GTDB search result was written to GCF_016638705.1_ASM1663870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:54,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:54,420] [INFO] DFAST_QC result json was written to GCF_016638705.1_ASM1663870v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:54,420] [INFO] DFAST_QC completed!
[2024-01-24 15:03:54,420] [INFO] Total running time: 0h1m30s