[2024-01-24 12:29:52,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference
[2024-01-24 12:29:53,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,915] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,916] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30d6115-7545-4888-9c54-e3064e4246ad/GCF_024266705.1_ASM2426670v1_genomic.fna.gz | prodigal -d GCF_024266705.1_ASM2426670v1_genomic.fna/cds.fna -a GCF_024266705.1_ASM2426670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:20,893] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:20,894] [INFO] Task started: HMMsearch
[2024-01-24 12:30:20,894] [INFO] Running command: hmmsearch --tblout GCF_024266705.1_ASM2426670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/reference_markers.hmm GCF_024266705.1_ASM2426670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:21,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:21,171] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf30d6115-7545-4888-9c54-e3064e4246ad/GCF_024266705.1_ASM2426670v1_genomic.fna.gz]
[2024-01-24 12:30:21,216] [INFO] Query marker FASTA was written to GCF_024266705.1_ASM2426670v1_genomic.fna/markers.fasta
[2024-01-24 12:30:21,216] [INFO] Task started: Blastn
[2024-01-24 12:30:21,217] [INFO] Running command: blastn -query GCF_024266705.1_ASM2426670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/reference_markers.fasta -out GCF_024266705.1_ASM2426670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:21,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:21,754] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:21,755] [INFO] Target genome list was writen to GCF_024266705.1_ASM2426670v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:21,763] [INFO] Task started: fastANI
[2024-01-24 12:30:21,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30d6115-7545-4888-9c54-e3064e4246ad/GCF_024266705.1_ASM2426670v1_genomic.fna.gz --refList GCF_024266705.1_ASM2426670v1_genomic.fna/target_genomes.txt --output GCF_024266705.1_ASM2426670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:30,344] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:30,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:30,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:30,360] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:30,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:30,360] [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
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	81.358	896	1813	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	81.2459	811	1813	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	80.9365	784	1813	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	80.9248	695	1813	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	80.7653	775	1813	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	80.6785	725	1813	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	80.646	795	1813	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	80.6279	787	1813	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	79.8752	704	1813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:30,362] [INFO] DFAST Taxonomy check result was written to GCF_024266705.1_ASM2426670v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:30,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:30,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:30,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/checkm_data
[2024-01-24 12:30:30,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:30,418] [INFO] Task started: CheckM
[2024-01-24 12:30:30,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024266705.1_ASM2426670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024266705.1_ASM2426670v1_genomic.fna/checkm_input GCF_024266705.1_ASM2426670v1_genomic.fna/checkm_result
[2024-01-24 12:31:42,593] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:42,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,620] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:42,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:42,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024266705.1_ASM2426670v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:42,622] [INFO] Task started: Blastn
[2024-01-24 12:31:42,622] [INFO] Running command: blastn -query GCF_024266705.1_ASM2426670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb7b656-bb19-466a-8171-2fe8f1ef4f43/dqc_reference/reference_markers_gtdb.fasta -out GCF_024266705.1_ASM2426670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:43,148] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:43,151] [INFO] Selected 9 target genomes.
[2024-01-24 12:31:43,151] [INFO] Target genome list was writen to GCF_024266705.1_ASM2426670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:43,158] [INFO] Task started: fastANI
[2024-01-24 12:31:43,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30d6115-7545-4888-9c54-e3064e4246ad/GCF_024266705.1_ASM2426670v1_genomic.fna.gz --refList GCF_024266705.1_ASM2426670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024266705.1_ASM2426670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:52,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:52,293] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:52,293] [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_013402815.1	s__Natrinema sp013402815	82.4332	933	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	81.363	894	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	81.221	837	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	81.0437	807	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_005938085.1	s__Natrinema sp005938085	80.9464	778	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337475.1	s__Natrinema limicola	80.907	697	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217335.1	s__Natrinema hispanicum	80.7862	774	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731985.1	s__Natrinema altunense	80.7381	736	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_900110455.1	s__Natrinema salifodinae	80.6384	796	1813	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:52,295] [INFO] GTDB search result was written to GCF_024266705.1_ASM2426670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:52,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:52,298] [INFO] DFAST_QC result json was written to GCF_024266705.1_ASM2426670v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:52,298] [INFO] DFAST_QC completed!
[2024-01-24 12:31:52,298] [INFO] Total running time: 0h1m60s