[2023-06-27 07:19:43,417] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:19:43,426] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:19:43,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference
[2023-06-27 07:19:44,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:19:44,694] [INFO] Task started: Prodigal
[2023-06-27 07:19:44,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9e3d755-d335-4ea4-b339-80afbe871c91/GCA_002403445.1_ASM240344v1_genomic.fna.gz | prodigal -d GCA_002403445.1_ASM240344v1_genomic.fna/cds.fna -a GCA_002403445.1_ASM240344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:19:50,389] [INFO] Task succeeded: Prodigal
[2023-06-27 07:19:50,390] [INFO] Task started: HMMsearch
[2023-06-27 07:19:50,390] [INFO] Running command: hmmsearch --tblout GCA_002403445.1_ASM240344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/reference_markers.hmm GCA_002403445.1_ASM240344v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:19:50,606] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:19:50,608] [INFO] Found 6/6 markers.
[2023-06-27 07:19:50,631] [INFO] Query marker FASTA was written to GCA_002403445.1_ASM240344v1_genomic.fna/markers.fasta
[2023-06-27 07:19:50,631] [INFO] Task started: Blastn
[2023-06-27 07:19:50,631] [INFO] Running command: blastn -query GCA_002403445.1_ASM240344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/reference_markers.fasta -out GCA_002403445.1_ASM240344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:19:51,338] [INFO] Task succeeded: Blastn
[2023-06-27 07:19:51,352] [INFO] Selected 23 target genomes.
[2023-06-27 07:19:51,352] [INFO] Target genome list was writen to GCA_002403445.1_ASM240344v1_genomic.fna/target_genomes.txt
[2023-06-27 07:19:51,357] [INFO] Task started: fastANI
[2023-06-27 07:19:51,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e3d755-d335-4ea4-b339-80afbe871c91/GCA_002403445.1_ASM240344v1_genomic.fna.gz --refList GCA_002403445.1_ASM240344v1_genomic.fna/target_genomes.txt --output GCA_002403445.1_ASM240344v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 07:20:04,568] [INFO] Task succeeded: fastANI
[2023-06-27 07:20:04,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 07:20:04,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 07:20:04,576] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 07:20:04,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 07:20:04,577] [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
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	77.1098	87	629	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.8862	88	629	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	76.793	60	629	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 07:20:04,579] [INFO] DFAST Taxonomy check result was written to GCA_002403445.1_ASM240344v1_genomic.fna/tc_result.tsv
[2023-06-27 07:20:04,580] [INFO] ===== Taxonomy check completed =====
[2023-06-27 07:20:04,580] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:20:04,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/checkm_data
[2023-06-27 07:20:04,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:20:04,621] [INFO] Task started: CheckM
[2023-06-27 07:20:04,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002403445.1_ASM240344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002403445.1_ASM240344v1_genomic.fna/checkm_input GCA_002403445.1_ASM240344v1_genomic.fna/checkm_result
[2023-06-27 07:20:28,175] [INFO] Task succeeded: CheckM
[2023-06-27 07:20:28,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:20:28,197] [INFO] ===== Completeness check finished =====
[2023-06-27 07:20:28,197] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:20:28,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002403445.1_ASM240344v1_genomic.fna/markers.fasta)
[2023-06-27 07:20:28,198] [INFO] Task started: Blastn
[2023-06-27 07:20:28,198] [INFO] Running command: blastn -query GCA_002403445.1_ASM240344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg176d9c79-8d69-412c-9dda-046138234310/dqc_reference/reference_markers_gtdb.fasta -out GCA_002403445.1_ASM240344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:20:29,414] [INFO] Task succeeded: Blastn
[2023-06-27 07:20:29,419] [INFO] Selected 28 target genomes.
[2023-06-27 07:20:29,420] [INFO] Target genome list was writen to GCA_002403445.1_ASM240344v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:20:29,433] [INFO] Task started: fastANI
[2023-06-27 07:20:29,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e3d755-d335-4ea4-b339-80afbe871c91/GCA_002403445.1_ASM240344v1_genomic.fna.gz --refList GCA_002403445.1_ASM240344v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002403445.1_ASM240344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:20:43,663] [INFO] Task succeeded: fastANI
[2023-06-27 07:20:43,672] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 07:20:43,673] [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
GCA_002403445.1	s__Salifodinibacter sp002403445	100.0	626	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salifodinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003177035.1	s__Salinisphaera sp003177035	77.322	94	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003732545.1	s__Salinisphaera halophila	77.1098	87	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	76.8862	88	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_012999515.1	s__Salifodinibacter halophilus	76.8706	113	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salifodinibacter	95.0	99.74	99.47	0.97	0.94	3	-
GCF_003788585.1	s__Salinisphaera japonica	76.793	60	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602005.1	s__Salinisphaera sp003602005	76.5388	64	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715985.1	s__Salinisphaera sp002715985	76.495	50	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	-
GCA_002729955.1	s__Salinisphaera sp002729955	76.4147	75	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	76.3645	83	629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:20:43,675] [INFO] GTDB search result was written to GCA_002403445.1_ASM240344v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:20:43,675] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:20:43,678] [INFO] DFAST_QC result json was written to GCA_002403445.1_ASM240344v1_genomic.fna/dqc_result.json
[2023-06-27 07:20:43,678] [INFO] DFAST_QC completed!
[2023-06-27 07:20:43,678] [INFO] Total running time: 0h1m0s