[2024-01-24 13:18:55,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,432] [INFO] DQC Reference Directory: /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference
[2024-01-24 13:18:56,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,762] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg758c181d-1111-4d58-b41c-b8488eb04b63/GCF_009762275.1_ASM976227v1_genomic.fna.gz | prodigal -d GCF_009762275.1_ASM976227v1_genomic.fna/cds.fna -a GCF_009762275.1_ASM976227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:14,509] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:14,509] [INFO] Task started: HMMsearch
[2024-01-24 13:19:14,510] [INFO] Running command: hmmsearch --tblout GCF_009762275.1_ASM976227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/reference_markers.hmm GCF_009762275.1_ASM976227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:14,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:14,763] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg758c181d-1111-4d58-b41c-b8488eb04b63/GCF_009762275.1_ASM976227v1_genomic.fna.gz]
[2024-01-24 13:19:14,804] [INFO] Query marker FASTA was written to GCF_009762275.1_ASM976227v1_genomic.fna/markers.fasta
[2024-01-24 13:19:14,804] [INFO] Task started: Blastn
[2024-01-24 13:19:14,804] [INFO] Running command: blastn -query GCF_009762275.1_ASM976227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/reference_markers.fasta -out GCF_009762275.1_ASM976227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:15,373] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:15,377] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:15,378] [INFO] Target genome list was writen to GCF_009762275.1_ASM976227v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:15,385] [INFO] Task started: fastANI
[2024-01-24 13:19:15,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg758c181d-1111-4d58-b41c-b8488eb04b63/GCF_009762275.1_ASM976227v1_genomic.fna.gz --refList GCF_009762275.1_ASM976227v1_genomic.fna/target_genomes.txt --output GCF_009762275.1_ASM976227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:22,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:22,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:22,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:22,616] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:22,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:22,617] [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
Haloplanus ruber	strain=R35	GCA_024494725.1	869892	869892	type	True	88.5646	801	1186	95	below_threshold
Haloplanus rubicundus	strain=CBA1112	GCA_003342675.1	1547898	1547898	type	True	84.6403	789	1186	95	below_threshold
Haloplanus salinus	strain=JCM 18368	GCA_003336245.1	1126245	1126245	type	True	84.0228	727	1186	95	below_threshold
Haloplanus natans	strain=DSM 17983	GCA_000427685.1	376171	376171	type	True	84.0161	755	1186	95	below_threshold
Haloplanus aerogenes	strain=JCM 16430	GCA_003856835.1	660522	660522	type	True	83.926	729	1186	95	below_threshold
Haloplanus aerogenes	strain=CGMCC 1.10124	GCA_003688715.1	660522	660522	type	True	83.8093	724	1186	95	below_threshold
Haloplanus vescus	strain=CGMCC 1.8712	GCA_900107665.1	555874	555874	type	True	83.299	642	1186	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	78.3432	453	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,618] [INFO] DFAST Taxonomy check result was written to GCF_009762275.1_ASM976227v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:22,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:22,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:22,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/checkm_data
[2024-01-24 13:19:22,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:22,662] [INFO] Task started: CheckM
[2024-01-24 13:19:22,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009762275.1_ASM976227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009762275.1_ASM976227v1_genomic.fna/checkm_input GCF_009762275.1_ASM976227v1_genomic.fna/checkm_result
[2024-01-24 13:20:11,153] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:11,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:11,177] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:11,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:11,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009762275.1_ASM976227v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:11,179] [INFO] Task started: Blastn
[2024-01-24 13:20:11,179] [INFO] Running command: blastn -query GCF_009762275.1_ASM976227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge29f5abb-8741-4d70-b6cf-7e91863023a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009762275.1_ASM976227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:11,777] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:11,781] [INFO] Selected 7 target genomes.
[2024-01-24 13:20:11,781] [INFO] Target genome list was writen to GCF_009762275.1_ASM976227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:11,806] [INFO] Task started: fastANI
[2024-01-24 13:20:11,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg758c181d-1111-4d58-b41c-b8488eb04b63/GCF_009762275.1_ASM976227v1_genomic.fna.gz --refList GCF_009762275.1_ASM976227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009762275.1_ASM976227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:18,512] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:18,524] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:18,525] [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_009762275.1	s__Haloplanus rallus	100.0	1183	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003342675.1	s__Haloplanus rubicundus	84.6532	788	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	98.71	98.71	0.88	0.88	2	-
GCF_003336245.1	s__Haloplanus salinus	84.0005	728	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427685.1	s__Haloplanus natans	83.9484	761	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856835.1	s__Haloplanus aerogenes	83.9021	731	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107665.1	s__Haloplanus vescus	83.2684	649	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	78.3176	459	1186	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:18,526] [INFO] GTDB search result was written to GCF_009762275.1_ASM976227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:18,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:18,529] [INFO] DFAST_QC result json was written to GCF_009762275.1_ASM976227v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:18,529] [INFO] DFAST_QC completed!
[2024-01-24 13:20:18,529] [INFO] Total running time: 0h1m23s