[2024-01-24 11:43:53,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference
[2024-01-24 11:43:54,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,533] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg13de3dbe-9dff-47c6-9421-71b67c52a158/GCF_025000405.1_ASM2500040v1_genomic.fna.gz | prodigal -d GCF_025000405.1_ASM2500040v1_genomic.fna/cds.fna -a GCF_025000405.1_ASM2500040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:04,043] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:04,043] [INFO] Task started: HMMsearch
[2024-01-24 11:44:04,043] [INFO] Running command: hmmsearch --tblout GCF_025000405.1_ASM2500040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/reference_markers.hmm GCF_025000405.1_ASM2500040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:04,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:04,253] [INFO] Found 6/6 markers.
[2024-01-24 11:44:04,283] [INFO] Query marker FASTA was written to GCF_025000405.1_ASM2500040v1_genomic.fna/markers.fasta
[2024-01-24 11:44:04,283] [INFO] Task started: Blastn
[2024-01-24 11:44:04,283] [INFO] Running command: blastn -query GCF_025000405.1_ASM2500040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/reference_markers.fasta -out GCF_025000405.1_ASM2500040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,436] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,440] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:05,440] [INFO] Target genome list was writen to GCF_025000405.1_ASM2500040v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,443] [INFO] Task started: fastANI
[2024-01-24 11:44:05,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg13de3dbe-9dff-47c6-9421-71b67c52a158/GCF_025000405.1_ASM2500040v1_genomic.fna.gz --refList GCF_025000405.1_ASM2500040v1_genomic.fna/target_genomes.txt --output GCF_025000405.1_ASM2500040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:12,462] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:12,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:12,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:12,471] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:12,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:12,472] [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 herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	100.0	1159	1160	95	conclusive
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	99.999	1159	1160	95	conclusive
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	85.0211	875	1160	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG 3645	GCA_013359815.1	2035	2035	suspected-type	True	85.0127	861	1160	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	84.9629	872	1160	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	84.6857	825	1160	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	84.6269	855	1160	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	84.525	855	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:12,473] [INFO] DFAST Taxonomy check result was written to GCF_025000405.1_ASM2500040v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:12,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:12,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:12,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/checkm_data
[2024-01-24 11:44:12,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:12,510] [INFO] Task started: CheckM
[2024-01-24 11:44:12,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025000405.1_ASM2500040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025000405.1_ASM2500040v1_genomic.fna/checkm_input GCF_025000405.1_ASM2500040v1_genomic.fna/checkm_result
[2024-01-24 11:45:02,648] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:02,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:02,665] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:02,665] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:02,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025000405.1_ASM2500040v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:02,666] [INFO] Task started: Blastn
[2024-01-24 11:45:02,666] [INFO] Running command: blastn -query GCF_025000405.1_ASM2500040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgead2d5e5-e327-4b45-bd7d-d3f486f181b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025000405.1_ASM2500040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:04,530] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:04,533] [INFO] Selected 8 target genomes.
[2024-01-24 11:45:04,533] [INFO] Target genome list was writen to GCF_025000405.1_ASM2500040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:04,538] [INFO] Task started: fastANI
[2024-01-24 11:45:04,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg13de3dbe-9dff-47c6-9421-71b67c52a158/GCF_025000405.1_ASM2500040v1_genomic.fna.gz --refList GCF_025000405.1_ASM2500040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025000405.1_ASM2500040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:12,044] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:12,052] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:12,052] [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_016907335.1	s__Curtobacterium herbarum	99.999	1159	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003234795.1	s__Curtobacterium sp003234795	93.474	1037	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759505.1	s__Curtobacterium flaccumfaciens_C	92.123	978	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234085.1	s__Curtobacterium sp003234085	91.357	949	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.77	96.93	0.92	0.88	6	-
GCF_018885305.1	s__Curtobacterium sp018885305	88.167	919	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234265.1	s__Curtobacterium sp003234265	88.1114	884	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.44	98.44	0.90	0.90	2	-
GCF_003224335.1	s__Curtobacterium sp003224335	87.7123	895	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	99.04	98.17	0.96	0.91	8	-
GCF_003234855.1	s__Curtobacterium sp003234855	87.3628	899	1160	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 11:45:12,054] [INFO] GTDB search result was written to GCF_025000405.1_ASM2500040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:12,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:12,057] [INFO] DFAST_QC result json was written to GCF_025000405.1_ASM2500040v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:12,057] [INFO] DFAST_QC completed!
[2024-01-24 11:45:12,057] [INFO] Total running time: 0h1m19s