[2024-01-24 13:45:48,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference
[2024-01-24 13:45:50,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,101] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg65658037-7fa5-4300-909c-6a3baf016789/GCF_014144975.1_ASM1414497v1_genomic.fna.gz | prodigal -d GCF_014144975.1_ASM1414497v1_genomic.fna/cds.fna -a GCF_014144975.1_ASM1414497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:57,480] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:57,481] [INFO] Task started: HMMsearch
[2024-01-24 13:45:57,481] [INFO] Running command: hmmsearch --tblout GCF_014144975.1_ASM1414497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/reference_markers.hmm GCF_014144975.1_ASM1414497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:57,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:57,735] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65658037-7fa5-4300-909c-6a3baf016789/GCF_014144975.1_ASM1414497v1_genomic.fna.gz]
[2024-01-24 13:45:57,763] [INFO] Query marker FASTA was written to GCF_014144975.1_ASM1414497v1_genomic.fna/markers.fasta
[2024-01-24 13:45:57,763] [INFO] Task started: Blastn
[2024-01-24 13:45:57,764] [INFO] Running command: blastn -query GCF_014144975.1_ASM1414497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/reference_markers.fasta -out GCF_014144975.1_ASM1414497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:58,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:58,892] [INFO] Selected 6 target genomes.
[2024-01-24 13:45:58,892] [INFO] Target genome list was writen to GCF_014144975.1_ASM1414497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:58,899] [INFO] Task started: fastANI
[2024-01-24 13:45:58,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg65658037-7fa5-4300-909c-6a3baf016789/GCF_014144975.1_ASM1414497v1_genomic.fna.gz --refList GCF_014144975.1_ASM1414497v1_genomic.fna/target_genomes.txt --output GCF_014144975.1_ASM1414497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:02,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:02,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:02,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:02,752] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:46:02,752] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:02,752] [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
Dietzia kunjamensis subsp. schimae	strain=YIM 65001T	GCA_014144975.1	498198	322509	type	True	99.9999	632	642	95	inconclusive
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	99.9934	641	642	95	inconclusive
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	96.7102	523	642	95	inconclusive
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	96.6634	565	642	95	inconclusive
Dietzia maris	strain=IMV 195T	GCA_014144855.1	37915	37915	suspected-type	True	96.4245	495	642	95	inconclusive
Dietzia maris	strain=IMV 195	GCA_009806365.1	37915	37915	suspected-type	True	96.4011	504	642	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 13:46:02,755] [INFO] DFAST Taxonomy check result was written to GCF_014144975.1_ASM1414497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:02,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:02,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:02,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/checkm_data
[2024-01-24 13:46:02,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:02,794] [INFO] Task started: CheckM
[2024-01-24 13:46:02,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014144975.1_ASM1414497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014144975.1_ASM1414497v1_genomic.fna/checkm_input GCF_014144975.1_ASM1414497v1_genomic.fna/checkm_result
[2024-01-24 13:46:30,220] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:30,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:30,239] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:30,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:30,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014144975.1_ASM1414497v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:30,240] [INFO] Task started: Blastn
[2024-01-24 13:46:30,240] [INFO] Running command: blastn -query GCF_014144975.1_ASM1414497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e1ca9bd-ca06-442c-b07a-c4ed79a963cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014144975.1_ASM1414497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:31,830] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:31,833] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:31,833] [INFO] Target genome list was writen to GCF_014144975.1_ASM1414497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:31,837] [INFO] Task started: fastANI
[2024-01-24 13:46:31,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg65658037-7fa5-4300-909c-6a3baf016789/GCF_014144975.1_ASM1414497v1_genomic.fna.gz --refList GCF_014144975.1_ASM1414497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014144975.1_ASM1414497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:36,910] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:36,917] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:36,917] [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_014144855.1	s__Dietzia maris	96.4245	495	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	87.0175	497	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
GCF_001571065.1	s__Dietzia cinnamea	86.31	511	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	-
GCF_003096075.1	s__Dietzia lutea	86.0503	508	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008369165.1	s__Dietzia sp008369165	85.9969	478	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145145.1	s__Dietzia cercidiphylli	84.7455	446	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.02	96.60	0.78	0.68	10	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	83.9126	467	642	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:36,919] [INFO] GTDB search result was written to GCF_014144975.1_ASM1414497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:36,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:36,922] [INFO] DFAST_QC result json was written to GCF_014144975.1_ASM1414497v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:36,922] [INFO] DFAST_QC completed!
[2024-01-24 13:46:36,922] [INFO] Total running time: 0h0m48s