[2023-06-27 18:42:38,819] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:42:38,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:42:38,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference
[2023-06-27 18:42:40,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:42:40,451] [INFO] Task started: Prodigal
[2023-06-27 18:42:40,451] [INFO] Running command: gunzip -c /var/lib/cwl/stge148735f-ef09-4160-9a12-8a237626dc52/GCA_027010785.1_ASM2701078v1_genomic.fna.gz | prodigal -d GCA_027010785.1_ASM2701078v1_genomic.fna/cds.fna -a GCA_027010785.1_ASM2701078v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:42:46,155] [INFO] Task succeeded: Prodigal
[2023-06-27 18:42:46,155] [INFO] Task started: HMMsearch
[2023-06-27 18:42:46,155] [INFO] Running command: hmmsearch --tblout GCA_027010785.1_ASM2701078v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/reference_markers.hmm GCA_027010785.1_ASM2701078v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:42:46,430] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:42:46,432] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge148735f-ef09-4160-9a12-8a237626dc52/GCA_027010785.1_ASM2701078v1_genomic.fna.gz]
[2023-06-27 18:42:46,463] [INFO] Query marker FASTA was written to GCA_027010785.1_ASM2701078v1_genomic.fna/markers.fasta
[2023-06-27 18:42:46,463] [INFO] Task started: Blastn
[2023-06-27 18:42:46,463] [INFO] Running command: blastn -query GCA_027010785.1_ASM2701078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/reference_markers.fasta -out GCA_027010785.1_ASM2701078v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:42:47,107] [INFO] Task succeeded: Blastn
[2023-06-27 18:42:47,111] [INFO] Selected 20 target genomes.
[2023-06-27 18:42:47,111] [INFO] Target genome list was writen to GCA_027010785.1_ASM2701078v1_genomic.fna/target_genomes.txt
[2023-06-27 18:42:47,117] [INFO] Task started: fastANI
[2023-06-27 18:42:47,117] [INFO] Running command: fastANI --query /var/lib/cwl/stge148735f-ef09-4160-9a12-8a237626dc52/GCA_027010785.1_ASM2701078v1_genomic.fna.gz --refList GCA_027010785.1_ASM2701078v1_genomic.fna/target_genomes.txt --output GCA_027010785.1_ASM2701078v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:43:01,070] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:01,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:43:01,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:43:01,072] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:43:01,072] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 18:43:01,072] [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
--------------------------------------------------------------------------------
[2023-06-27 18:43:01,078] [INFO] DFAST Taxonomy check result was written to GCA_027010785.1_ASM2701078v1_genomic.fna/tc_result.tsv
[2023-06-27 18:43:01,078] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:43:01,079] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:43:01,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/checkm_data
[2023-06-27 18:43:01,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:43:01,120] [INFO] Task started: CheckM
[2023-06-27 18:43:01,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027010785.1_ASM2701078v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027010785.1_ASM2701078v1_genomic.fna/checkm_input GCA_027010785.1_ASM2701078v1_genomic.fna/checkm_result
[2023-06-27 18:43:25,245] [INFO] Task succeeded: CheckM
[2023-06-27 18:43:25,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.25%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:43:25,268] [INFO] ===== Completeness check finished =====
[2023-06-27 18:43:25,268] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:43:25,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027010785.1_ASM2701078v1_genomic.fna/markers.fasta)
[2023-06-27 18:43:25,269] [INFO] Task started: Blastn
[2023-06-27 18:43:25,269] [INFO] Running command: blastn -query GCA_027010785.1_ASM2701078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7217e1ac-5ae5-4599-ae07-8f9b0e5a05a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_027010785.1_ASM2701078v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:26,107] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:26,110] [INFO] Selected 14 target genomes.
[2023-06-27 18:43:26,111] [INFO] Target genome list was writen to GCA_027010785.1_ASM2701078v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:43:26,121] [INFO] Task started: fastANI
[2023-06-27 18:43:26,121] [INFO] Running command: fastANI --query /var/lib/cwl/stge148735f-ef09-4160-9a12-8a237626dc52/GCA_027010785.1_ASM2701078v1_genomic.fna.gz --refList GCA_027010785.1_ASM2701078v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027010785.1_ASM2701078v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:43:33,230] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:33,240] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:43:33,240] [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_015489765.1	s__DRLX01 sp015489765	94.6179	215	226	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011322715.1	s__DRLX01 sp011322715	84.2855	172	226	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	98.07	98.07	0.69	0.69	2	-
GCA_015493715.1	s__DRLX01 sp015493715	83.5839	194	226	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051825.1	s__DRLX01 sp011051825	77.6923	77	226	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484845.1	s__DRKI01 sp015484845	77.1702	59	226	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:43:33,242] [INFO] GTDB search result was written to GCA_027010785.1_ASM2701078v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:43:33,242] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:43:33,245] [INFO] DFAST_QC result json was written to GCA_027010785.1_ASM2701078v1_genomic.fna/dqc_result.json
[2023-06-27 18:43:33,245] [INFO] DFAST_QC completed!
[2023-06-27 18:43:33,245] [INFO] Total running time: 0h0m54s