[2024-01-24 13:17:33,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference
[2024-01-24 13:17:35,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,051] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,052] [INFO] Running command: gunzip -c /var/lib/cwl/stg41d63a5f-ec06-4982-b648-e9a62632d83d/GCF_006715175.1_ASM671517v1_genomic.fna.gz | prodigal -d GCF_006715175.1_ASM671517v1_genomic.fna/cds.fna -a GCF_006715175.1_ASM671517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:45,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:45,252] [INFO] Task started: HMMsearch
[2024-01-24 13:17:45,252] [INFO] Running command: hmmsearch --tblout GCF_006715175.1_ASM671517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/reference_markers.hmm GCF_006715175.1_ASM671517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,525] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,560] [INFO] Query marker FASTA was written to GCF_006715175.1_ASM671517v1_genomic.fna/markers.fasta
[2024-01-24 13:17:45,560] [INFO] Task started: Blastn
[2024-01-24 13:17:45,561] [INFO] Running command: blastn -query GCF_006715175.1_ASM671517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/reference_markers.fasta -out GCF_006715175.1_ASM671517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:46,818] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:46,823] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:46,824] [INFO] Target genome list was writen to GCF_006715175.1_ASM671517v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:46,829] [INFO] Task started: fastANI
[2024-01-24 13:17:46,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d63a5f-ec06-4982-b648-e9a62632d83d/GCF_006715175.1_ASM671517v1_genomic.fna.gz --refList GCF_006715175.1_ASM671517v1_genomic.fna/target_genomes.txt --output GCF_006715175.1_ASM671517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:57,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:57,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:57,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:57,131] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:17:57,132] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:17:57,132] [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 citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	100.0	1204	1204	95	inconclusive
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	99.9894	1186	1204	95	inconclusive
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	99.9817	1183	1204	95	inconclusive
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	97.2844	1042	1204	95	inconclusive
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	85.9769	911	1204	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	85.9489	904	1204	95	below_threshold
Curtobacterium pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	85.9416	843	1204	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	85.688	912	1204	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	85.5018	909	1204	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	84.7413	863	1204	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	84.6735	846	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:57,133] [INFO] DFAST Taxonomy check result was written to GCF_006715175.1_ASM671517v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:57,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:57,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:57,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/checkm_data
[2024-01-24 13:17:57,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:57,172] [INFO] Task started: CheckM
[2024-01-24 13:17:57,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006715175.1_ASM671517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006715175.1_ASM671517v1_genomic.fna/checkm_input GCF_006715175.1_ASM671517v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,114] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,136] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006715175.1_ASM671517v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,137] [INFO] Task started: Blastn
[2024-01-24 13:19:00,137] [INFO] Running command: blastn -query GCF_006715175.1_ASM671517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f1cc9f1-8b1a-4889-9174-c0fa274d5f82/dqc_reference/reference_markers_gtdb.fasta -out GCF_006715175.1_ASM671517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:02,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:02,109] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:02,109] [INFO] Target genome list was writen to GCF_006715175.1_ASM671517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:02,119] [INFO] Task started: fastANI
[2024-01-24 13:19:02,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d63a5f-ec06-4982-b648-e9a62632d83d/GCF_006715175.1_ASM671517v1_genomic.fna.gz --refList GCF_006715175.1_ASM671517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006715175.1_ASM671517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:12,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:12,471] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:12,471] [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_006715175.1	s__Curtobacterium citreum	100.0	1203	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.94	96.06	0.93	0.88	10	conclusive
GCF_001705035.1	s__Curtobacterium sp001705035	88.1069	868	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.77	98.72	0.93	0.91	3	-
GCF_003989515.1	s__Curtobacterium sp003989515	87.9054	834	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.86	98.78	0.96	0.96	3	-
GCF_005490985.1	s__Curtobacterium oceanosedimentum	87.8997	954	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.58	95.49	0.91	0.91	3	-
GCF_001742745.1	s__Curtobacterium sp001742745	87.6886	908	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.38	97.38	0.89	0.89	2	-
GCF_000772085.1	s__Curtobacterium sp000772085	87.5404	951	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.95	98.95	0.96	0.96	2	-
GCF_003234175.1	s__Curtobacterium sp003234175	87.4984	919	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234185.1	s__Curtobacterium sp003234185	87.4776	872	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	86.3198	926	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_007680845.1	s__Curtobacterium pusillum_B	85.9176	886	1204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018885305.1	s__Curtobacterium sp018885305	84.6728	839	1204	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 13:19:12,473] [INFO] GTDB search result was written to GCF_006715175.1_ASM671517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:12,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:12,478] [INFO] DFAST_QC result json was written to GCF_006715175.1_ASM671517v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:12,479] [INFO] DFAST_QC completed!
[2024-01-24 13:19:12,479] [INFO] Total running time: 0h1m39s