[2024-01-24 13:37:12,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:12,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:12,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference
[2024-01-24 13:37:14,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,232] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,232] [INFO] Running command: gunzip -c /var/lib/cwl/stge7672a4b-34b0-41f7-aecd-d13602419b29/GCF_009806405.1_ASM980640v1_genomic.fna.gz | prodigal -d GCF_009806405.1_ASM980640v1_genomic.fna/cds.fna -a GCF_009806405.1_ASM980640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:21,478] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:21,479] [INFO] Task started: HMMsearch
[2024-01-24 13:37:21,479] [INFO] Running command: hmmsearch --tblout GCF_009806405.1_ASM980640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/reference_markers.hmm GCF_009806405.1_ASM980640v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:21,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:21,710] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge7672a4b-34b0-41f7-aecd-d13602419b29/GCF_009806405.1_ASM980640v1_genomic.fna.gz]
[2024-01-24 13:37:21,742] [INFO] Query marker FASTA was written to GCF_009806405.1_ASM980640v1_genomic.fna/markers.fasta
[2024-01-24 13:37:21,742] [INFO] Task started: Blastn
[2024-01-24 13:37:21,743] [INFO] Running command: blastn -query GCF_009806405.1_ASM980640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/reference_markers.fasta -out GCF_009806405.1_ASM980640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:22,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:22,872] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:22,873] [INFO] Target genome list was writen to GCF_009806405.1_ASM980640v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:22,885] [INFO] Task started: fastANI
[2024-01-24 13:37:22,886] [INFO] Running command: fastANI --query /var/lib/cwl/stge7672a4b-34b0-41f7-aecd-d13602419b29/GCF_009806405.1_ASM980640v1_genomic.fna.gz --refList GCF_009806405.1_ASM980640v1_genomic.fna/target_genomes.txt --output GCF_009806405.1_ASM980640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:27,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:27,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:27,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:27,710] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:27,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:27,711] [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 lutea	strain=YIM 80766	GCA_009806405.1	546160	546160	type	True	100.0	715	731	95	conclusive
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	99.9929	730	731	95	conclusive
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	93.2186	569	731	95	below_threshold
Dietzia cinnamea	strain=NBRC 102147	GCA_001571065.1	321318	321318	type	True	92.8753	557	731	95	below_threshold
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	86.1221	476	731	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	86.0512	545	731	95	below_threshold
Dietzia maris	strain=IMV 195T	GCA_014144855.1	37915	37915	suspected-type	True	85.955	467	731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,712] [INFO] DFAST Taxonomy check result was written to GCF_009806405.1_ASM980640v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:27,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:27,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:27,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/checkm_data
[2024-01-24 13:37:27,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:27,750] [INFO] Task started: CheckM
[2024-01-24 13:37:27,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009806405.1_ASM980640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009806405.1_ASM980640v1_genomic.fna/checkm_input GCF_009806405.1_ASM980640v1_genomic.fna/checkm_result
[2024-01-24 13:37:54,769] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:54,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:54,791] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:54,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:54,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009806405.1_ASM980640v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:54,792] [INFO] Task started: Blastn
[2024-01-24 13:37:54,792] [INFO] Running command: blastn -query GCF_009806405.1_ASM980640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbfe88b0-834d-43bc-bbee-c4d00c45d728/dqc_reference/reference_markers_gtdb.fasta -out GCF_009806405.1_ASM980640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:56,557] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:56,561] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:56,561] [INFO] Target genome list was writen to GCF_009806405.1_ASM980640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:56,570] [INFO] Task started: fastANI
[2024-01-24 13:37:56,571] [INFO] Running command: fastANI --query /var/lib/cwl/stge7672a4b-34b0-41f7-aecd-d13602419b29/GCF_009806405.1_ASM980640v1_genomic.fna.gz --refList GCF_009806405.1_ASM980640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009806405.1_ASM980640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:01,270] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:01,277] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:01,277] [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_003096075.1	s__Dietzia lutea	99.9929	730	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	93.3108	561	731	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	92.8753	557	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	-
GCF_014144855.1	s__Dietzia maris	85.955	467	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	-
GCF_008369165.1	s__Dietzia sp008369165	84.1168	480	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841845.1	s__Dietzia sp012841845	83.663	352	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014144865.1	s__Dietzia aerolata	83.0644	440	731	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.62	97.62	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:01,279] [INFO] GTDB search result was written to GCF_009806405.1_ASM980640v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:01,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:01,283] [INFO] DFAST_QC result json was written to GCF_009806405.1_ASM980640v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:01,283] [INFO] DFAST_QC completed!
[2024-01-24 13:38:01,284] [INFO] Total running time: 0h0m48s