[2023-06-17 03:13:33,504] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:13:33,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:13:33,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference
[2023-06-17 03:13:35,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:13:35,444] [INFO] Task started: Prodigal
[2023-06-17 03:13:35,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg6aa079df-f2ea-4200-8145-c2ad05d72d3b/GCA_003531135.1_ASM353113v1_genomic.fna.gz | prodigal -d GCA_003531135.1_ASM353113v1_genomic.fna/cds.fna -a GCA_003531135.1_ASM353113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:13:51,097] [INFO] Task succeeded: Prodigal
[2023-06-17 03:13:51,097] [INFO] Task started: HMMsearch
[2023-06-17 03:13:51,097] [INFO] Running command: hmmsearch --tblout GCA_003531135.1_ASM353113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/reference_markers.hmm GCA_003531135.1_ASM353113v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:13:51,407] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:13:51,409] [INFO] Found 6/6 markers.
[2023-06-17 03:13:51,463] [INFO] Query marker FASTA was written to GCA_003531135.1_ASM353113v1_genomic.fna/markers.fasta
[2023-06-17 03:13:51,463] [INFO] Task started: Blastn
[2023-06-17 03:13:51,464] [INFO] Running command: blastn -query GCA_003531135.1_ASM353113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/reference_markers.fasta -out GCA_003531135.1_ASM353113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:13:52,074] [INFO] Task succeeded: Blastn
[2023-06-17 03:13:52,078] [INFO] Selected 19 target genomes.
[2023-06-17 03:13:52,078] [INFO] Target genome list was writen to GCA_003531135.1_ASM353113v1_genomic.fna/target_genomes.txt
[2023-06-17 03:13:52,124] [INFO] Task started: fastANI
[2023-06-17 03:13:52,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aa079df-f2ea-4200-8145-c2ad05d72d3b/GCA_003531135.1_ASM353113v1_genomic.fna.gz --refList GCA_003531135.1_ASM353113v1_genomic.fna/target_genomes.txt --output GCA_003531135.1_ASM353113v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:14:10,328] [INFO] Task succeeded: fastANI
[2023-06-17 03:14:10,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:14:10,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:14:10,341] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:14:10,342] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:14:10,342] [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
Rubinisphaera italica	strain=Pan54	GCA_007859715.1	2527969	2527969	type	True	85.9664	1525	2015	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	76.3233	252	2015	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	76.057	154	2015	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:14:10,344] [INFO] DFAST Taxonomy check result was written to GCA_003531135.1_ASM353113v1_genomic.fna/tc_result.tsv
[2023-06-17 03:14:10,345] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:14:10,345] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:14:10,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/checkm_data
[2023-06-17 03:14:10,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:14:10,426] [INFO] Task started: CheckM
[2023-06-17 03:14:10,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003531135.1_ASM353113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003531135.1_ASM353113v1_genomic.fna/checkm_input GCA_003531135.1_ASM353113v1_genomic.fna/checkm_result
[2023-06-17 03:14:57,665] [INFO] Task succeeded: CheckM
[2023-06-17 03:14:57,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:14:57,692] [INFO] ===== Completeness check finished =====
[2023-06-17 03:14:57,692] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:14:57,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003531135.1_ASM353113v1_genomic.fna/markers.fasta)
[2023-06-17 03:14:57,693] [INFO] Task started: Blastn
[2023-06-17 03:14:57,693] [INFO] Running command: blastn -query GCA_003531135.1_ASM353113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22db5a9a-1a58-4462-a6a0-59d2e3745466/dqc_reference/reference_markers_gtdb.fasta -out GCA_003531135.1_ASM353113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:14:58,587] [INFO] Task succeeded: Blastn
[2023-06-17 03:14:58,592] [INFO] Selected 16 target genomes.
[2023-06-17 03:14:58,592] [INFO] Target genome list was writen to GCA_003531135.1_ASM353113v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:14:58,607] [INFO] Task started: fastANI
[2023-06-17 03:14:58,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aa079df-f2ea-4200-8145-c2ad05d72d3b/GCA_003531135.1_ASM353113v1_genomic.fna.gz --refList GCA_003531135.1_ASM353113v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003531135.1_ASM353113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:15:18,007] [INFO] Task succeeded: fastANI
[2023-06-17 03:15:18,017] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 03:15:18,017] [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_002359185.1	s__Rubinisphaera sp002359185	99.7441	1879	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	99.90	99.90	0.94	0.94	2	conclusive
GCF_007859715.1	s__Rubinisphaera italica	85.9403	1529	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	76.3484	228	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	76.078	152	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765335.1	s__Rubinisphaera sp016765335	75.8107	60	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584345.1	s__Rubinisphaera sp014584345	75.5344	110	2015	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:15:18,019] [INFO] GTDB search result was written to GCA_003531135.1_ASM353113v1_genomic.fna/result_gtdb.tsv
[2023-06-17 03:15:18,020] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:15:18,023] [INFO] DFAST_QC result json was written to GCA_003531135.1_ASM353113v1_genomic.fna/dqc_result.json
[2023-06-17 03:15:18,023] [INFO] DFAST_QC completed!
[2023-06-17 03:15:18,023] [INFO] Total running time: 0h1m45s