[2024-01-24 11:35:11,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,498] [INFO] DQC Reference Directory: /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference
[2024-01-24 11:35:12,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,808] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg78e77933-87ac-4182-b30e-0d14390eb64e/GCF_013359865.1_ASM1335986v1_genomic.fna.gz | prodigal -d GCF_013359865.1_ASM1335986v1_genomic.fna/cds.fna -a GCF_013359865.1_ASM1335986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,691] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,691] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,691] [INFO] Running command: hmmsearch --tblout GCF_013359865.1_ASM1335986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/reference_markers.hmm GCF_013359865.1_ASM1335986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,996] [INFO] Found 6/6 markers.
[2024-01-24 11:35:23,036] [INFO] Query marker FASTA was written to GCF_013359865.1_ASM1335986v1_genomic.fna/markers.fasta
[2024-01-24 11:35:23,037] [INFO] Task started: Blastn
[2024-01-24 11:35:23,037] [INFO] Running command: blastn -query GCF_013359865.1_ASM1335986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/reference_markers.fasta -out GCF_013359865.1_ASM1335986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:24,241] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:24,244] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:24,245] [INFO] Target genome list was writen to GCF_013359865.1_ASM1335986v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:24,250] [INFO] Task started: fastANI
[2024-01-24 11:35:24,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e77933-87ac-4182-b30e-0d14390eb64e/GCF_013359865.1_ASM1335986v1_genomic.fna.gz --refList GCF_013359865.1_ASM1335986v1_genomic.fna/target_genomes.txt --output GCF_013359865.1_ASM1335986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:35,769] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:35,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:35,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:35,781] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:35,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:35,782] [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 pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	100.0	1162	1167	95	conclusive
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	86.3366	888	1167	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG 3645	GCA_013359815.1	2035	2035	suspected-type	True	86.3224	882	1167	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	86.2677	891	1167	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	85.9856	839	1167	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	85.9736	819	1167	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	85.9611	822	1167	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	85.9312	813	1167	95	below_threshold
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	85.9005	870	1167	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	85.7661	856	1167	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	85.7648	856	1167	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	84.3896	784	1167	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	84.349	788	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:35,783] [INFO] DFAST Taxonomy check result was written to GCF_013359865.1_ASM1335986v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:35,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:35,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:35,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/checkm_data
[2024-01-24 11:35:35,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:35,824] [INFO] Task started: CheckM
[2024-01-24 11:35:35,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013359865.1_ASM1335986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013359865.1_ASM1335986v1_genomic.fna/checkm_input GCF_013359865.1_ASM1335986v1_genomic.fna/checkm_result
[2024-01-24 11:36:28,546] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:28,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,575] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:28,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:28,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013359865.1_ASM1335986v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:28,576] [INFO] Task started: Blastn
[2024-01-24 11:36:28,576] [INFO] Running command: blastn -query GCF_013359865.1_ASM1335986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge62ffbdf-3ed9-4c29-82cc-157f588d757e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013359865.1_ASM1335986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:30,459] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:30,463] [INFO] Selected 9 target genomes.
[2024-01-24 11:36:30,464] [INFO] Target genome list was writen to GCF_013359865.1_ASM1335986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:30,473] [INFO] Task started: fastANI
[2024-01-24 11:36:30,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e77933-87ac-4182-b30e-0d14390eb64e/GCF_013359865.1_ASM1335986v1_genomic.fna.gz --refList GCF_013359865.1_ASM1335986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013359865.1_ASM1335986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:39,194] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:39,205] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:39,205] [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_013359865.1	s__Curtobacterium pusillum	100.0	1162	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.75	98.75	0.92	0.92	2	conclusive
GCF_002025645.1	s__Curtobacterium pusillum_A	89.0044	968	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.99	95.99	0.91	0.91	2	-
GCF_001806325.1	s__Curtobacterium sp001806325	88.827	924	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_007673235.1	s__Curtobacterium pusillum_C	88.7963	940	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007680845.1	s__Curtobacterium pusillum_B	88.5261	931	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101675.1	s__Curtobacterium sp900101675	88.3757	933	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361695.1	s__Curtobacterium flaccumfaciens_B	88.3684	931	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865065.1	s__Curtobacterium sp001865065	88.1879	922	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333375.1	s__Curtobacterium sp000333375	87.6805	681	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:39,207] [INFO] GTDB search result was written to GCF_013359865.1_ASM1335986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:39,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:39,210] [INFO] DFAST_QC result json was written to GCF_013359865.1_ASM1335986v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:39,211] [INFO] DFAST_QC completed!
[2024-01-24 11:36:39,211] [INFO] Total running time: 0h1m28s