[2023-06-28 16:15:29,696] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:15:29,698] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:15:29,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference
[2023-06-28 16:15:30,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:15:30,855] [INFO] Task started: Prodigal
[2023-06-28 16:15:30,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eebed06-0851-4fc8-8bd2-95fbdaa47503/GCA_027405065.1_ASM2740506v1_genomic.fna.gz | prodigal -d GCA_027405065.1_ASM2740506v1_genomic.fna/cds.fna -a GCA_027405065.1_ASM2740506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:15:39,433] [INFO] Task succeeded: Prodigal
[2023-06-28 16:15:39,433] [INFO] Task started: HMMsearch
[2023-06-28 16:15:39,433] [INFO] Running command: hmmsearch --tblout GCA_027405065.1_ASM2740506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/reference_markers.hmm GCA_027405065.1_ASM2740506v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:15:39,602] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:15:39,604] [INFO] Found 6/6 markers.
[2023-06-28 16:15:39,628] [INFO] Query marker FASTA was written to GCA_027405065.1_ASM2740506v1_genomic.fna/markers.fasta
[2023-06-28 16:15:39,628] [INFO] Task started: Blastn
[2023-06-28 16:15:39,628] [INFO] Running command: blastn -query GCA_027405065.1_ASM2740506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/reference_markers.fasta -out GCA_027405065.1_ASM2740506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:15:40,234] [INFO] Task succeeded: Blastn
[2023-06-28 16:15:40,239] [INFO] Selected 26 target genomes.
[2023-06-28 16:15:40,239] [INFO] Target genome list was writen to GCA_027405065.1_ASM2740506v1_genomic.fna/target_genomes.txt
[2023-06-28 16:15:40,241] [INFO] Task started: fastANI
[2023-06-28 16:15:40,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eebed06-0851-4fc8-8bd2-95fbdaa47503/GCA_027405065.1_ASM2740506v1_genomic.fna.gz --refList GCA_027405065.1_ASM2740506v1_genomic.fna/target_genomes.txt --output GCA_027405065.1_ASM2740506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:15:55,029] [INFO] Task succeeded: fastANI
[2023-06-28 16:15:55,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:15:55,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:15:55,035] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:15:55,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:15:55,036] [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
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	76.6899	64	453	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	76.0854	54	453	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	75.9042	50	453	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	75.7016	51	453	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	75.6831	50	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:15:55,037] [INFO] DFAST Taxonomy check result was written to GCA_027405065.1_ASM2740506v1_genomic.fna/tc_result.tsv
[2023-06-28 16:15:55,038] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:15:55,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:15:55,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/checkm_data
[2023-06-28 16:15:55,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:15:55,062] [INFO] Task started: CheckM
[2023-06-28 16:15:55,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027405065.1_ASM2740506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027405065.1_ASM2740506v1_genomic.fna/checkm_input GCA_027405065.1_ASM2740506v1_genomic.fna/checkm_result
[2023-06-28 16:16:23,311] [INFO] Task succeeded: CheckM
[2023-06-28 16:16:23,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:16:23,337] [INFO] ===== Completeness check finished =====
[2023-06-28 16:16:23,338] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:16:23,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027405065.1_ASM2740506v1_genomic.fna/markers.fasta)
[2023-06-28 16:16:23,338] [INFO] Task started: Blastn
[2023-06-28 16:16:23,339] [INFO] Running command: blastn -query GCA_027405065.1_ASM2740506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf779cc1f-38b1-4eef-ae6f-a28c2b780f83/dqc_reference/reference_markers_gtdb.fasta -out GCA_027405065.1_ASM2740506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:16:24,175] [INFO] Task succeeded: Blastn
[2023-06-28 16:16:24,180] [INFO] Selected 27 target genomes.
[2023-06-28 16:16:24,180] [INFO] Target genome list was writen to GCA_027405065.1_ASM2740506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:16:24,184] [INFO] Task started: fastANI
[2023-06-28 16:16:24,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eebed06-0851-4fc8-8bd2-95fbdaa47503/GCA_027405065.1_ASM2740506v1_genomic.fna.gz --refList GCA_027405065.1_ASM2740506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027405065.1_ASM2740506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:16:38,453] [INFO] Task succeeded: fastANI
[2023-06-28 16:16:38,459] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:16:38,459] [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_014202645.1	s__Deinobacterium chartae	76.6899	64	453	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173015.1	s__Deinococcus irradiatisoli	76.054	55	453	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	75.7016	51	453	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	75.6831	50	453	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:16:38,461] [INFO] GTDB search result was written to GCA_027405065.1_ASM2740506v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:16:38,462] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:16:38,465] [INFO] DFAST_QC result json was written to GCA_027405065.1_ASM2740506v1_genomic.fna/dqc_result.json
[2023-06-28 16:16:38,466] [INFO] DFAST_QC completed!
[2023-06-28 16:16:38,466] [INFO] Total running time: 0h1m9s