[2024-01-24 12:22:14,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,003] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference
[2024-01-24 12:22:15,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,450] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg3145bc5f-46ce-437a-a9c2-83743efedb78/GCF_024997845.1_ASM2499784v1_genomic.fna.gz | prodigal -d GCF_024997845.1_ASM2499784v1_genomic.fna/cds.fna -a GCF_024997845.1_ASM2499784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:26,462] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:26,462] [INFO] Task started: HMMsearch
[2024-01-24 12:22:26,462] [INFO] Running command: hmmsearch --tblout GCF_024997845.1_ASM2499784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/reference_markers.hmm GCF_024997845.1_ASM2499784v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:26,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:26,804] [INFO] Found 6/6 markers.
[2024-01-24 12:22:26,856] [INFO] Query marker FASTA was written to GCF_024997845.1_ASM2499784v1_genomic.fna/markers.fasta
[2024-01-24 12:22:26,856] [INFO] Task started: Blastn
[2024-01-24 12:22:26,856] [INFO] Running command: blastn -query GCF_024997845.1_ASM2499784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/reference_markers.fasta -out GCF_024997845.1_ASM2499784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:28,185] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:28,189] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:28,189] [INFO] Target genome list was writen to GCF_024997845.1_ASM2499784v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:28,211] [INFO] Task started: fastANI
[2024-01-24 12:22:28,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg3145bc5f-46ce-437a-a9c2-83743efedb78/GCF_024997845.1_ASM2499784v1_genomic.fna.gz --refList GCF_024997845.1_ASM2499784v1_genomic.fna/target_genomes.txt --output GCF_024997845.1_ASM2499784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:37,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:37,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:37,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:37,989] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:37,989] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:22:37,989] [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
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	100.0	1270	1270	95	inconclusive
Curtobacterium flaccumfaciens	strain=LMG 3645	GCA_013359815.1	2035	2035	suspected-type	True	99.9949	1261	1270	95	inconclusive
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	96.083	1112	1270	95	inconclusive
Curtobacterium pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	86.4619	867	1270	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	85.5757	897	1270	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	85.5149	898	1270	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	85.4913	902	1270	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	85.2577	914	1270	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	85.1273	863	1270	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	85.1028	868	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,992] [INFO] DFAST Taxonomy check result was written to GCF_024997845.1_ASM2499784v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:37,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:37,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:37,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/checkm_data
[2024-01-24 12:22:37,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:38,035] [INFO] Task started: CheckM
[2024-01-24 12:22:38,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024997845.1_ASM2499784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024997845.1_ASM2499784v1_genomic.fna/checkm_input GCF_024997845.1_ASM2499784v1_genomic.fna/checkm_result
[2024-01-24 12:23:36,003] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:36,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,027] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:36,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:36,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024997845.1_ASM2499784v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:36,029] [INFO] Task started: Blastn
[2024-01-24 12:23:36,029] [INFO] Running command: blastn -query GCF_024997845.1_ASM2499784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4f2b7d9-4eea-4f56-997c-c05123f6905e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024997845.1_ASM2499784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:38,088] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:38,094] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:38,095] [INFO] Target genome list was writen to GCF_024997845.1_ASM2499784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:38,120] [INFO] Task started: fastANI
[2024-01-24 12:23:38,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg3145bc5f-46ce-437a-a9c2-83743efedb78/GCF_024997845.1_ASM2499784v1_genomic.fna.gz --refList GCF_024997845.1_ASM2499784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024997845.1_ASM2499784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:46,609] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:46,622] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:46,622] [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_013359815.1	s__Curtobacterium flaccumfaciens	99.9949	1261	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	96.92	95.24	0.91	0.86	53	conclusive
GCF_000349565.1	s__Curtobacterium flaccumfaciens_A	94.2864	1076	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.89	98.72	0.94	0.92	12	-
GCF_018598555.1	s__Curtobacterium flaccumfaciens_D	94.0221	1059	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.57	98.53	0.91	0.91	4	-
GCF_015351025.1	s__Curtobacterium sp015351025	91.193	986	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016267665.1	s__Curtobacterium sp016267665	90.0619	973	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015350995.1	s__Curtobacterium sp015350995	88.9396	1050	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752025.1	s__Curtobacterium sp003752025	88.6823	1014	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001864895.1	s__Curtobacterium sp001864895	88.3714	943	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.49	96.88	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:46,625] [INFO] GTDB search result was written to GCF_024997845.1_ASM2499784v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:46,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:46,628] [INFO] DFAST_QC result json was written to GCF_024997845.1_ASM2499784v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:46,628] [INFO] DFAST_QC completed!
[2024-01-24 12:23:46,628] [INFO] Total running time: 0h1m33s