[2023-06-19 08:40:18,168] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:40:18,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:40:18,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference
[2023-06-19 08:40:19,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:40:19,318] [INFO] Task started: Prodigal
[2023-06-19 08:40:19,318] [INFO] Running command: gunzip -c /var/lib/cwl/stg5695b601-2c83-468a-9871-68c93a521cca/GCA_018652385.1_ASM1865238v1_genomic.fna.gz | prodigal -d GCA_018652385.1_ASM1865238v1_genomic.fna/cds.fna -a GCA_018652385.1_ASM1865238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:40:20,984] [INFO] Task succeeded: Prodigal
[2023-06-19 08:40:20,985] [INFO] Task started: HMMsearch
[2023-06-19 08:40:20,985] [INFO] Running command: hmmsearch --tblout GCA_018652385.1_ASM1865238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/reference_markers.hmm GCA_018652385.1_ASM1865238v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:40:21,136] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:40:21,137] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5695b601-2c83-468a-9871-68c93a521cca/GCA_018652385.1_ASM1865238v1_genomic.fna.gz]
[2023-06-19 08:40:21,149] [INFO] Query marker FASTA was written to GCA_018652385.1_ASM1865238v1_genomic.fna/markers.fasta
[2023-06-19 08:40:21,149] [INFO] Task started: Blastn
[2023-06-19 08:40:21,149] [INFO] Running command: blastn -query GCA_018652385.1_ASM1865238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/reference_markers.fasta -out GCA_018652385.1_ASM1865238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:21,721] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:21,724] [INFO] Selected 14 target genomes.
[2023-06-19 08:40:21,725] [INFO] Target genome list was writen to GCA_018652385.1_ASM1865238v1_genomic.fna/target_genomes.txt
[2023-06-19 08:40:21,727] [INFO] Task started: fastANI
[2023-06-19 08:40:21,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg5695b601-2c83-468a-9871-68c93a521cca/GCA_018652385.1_ASM1865238v1_genomic.fna.gz --refList GCA_018652385.1_ASM1865238v1_genomic.fna/target_genomes.txt --output GCA_018652385.1_ASM1865238v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:40:28,337] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:28,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:40:28,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:40:28,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:40:28,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:40:28,340] [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
--------------------------------------------------------------------------------
[2023-06-19 08:40:28,342] [INFO] DFAST Taxonomy check result was written to GCA_018652385.1_ASM1865238v1_genomic.fna/tc_result.tsv
[2023-06-19 08:40:28,343] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:40:28,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:40:28,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/checkm_data
[2023-06-19 08:40:28,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:40:28,358] [INFO] Task started: CheckM
[2023-06-19 08:40:28,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018652385.1_ASM1865238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018652385.1_ASM1865238v1_genomic.fna/checkm_input GCA_018652385.1_ASM1865238v1_genomic.fna/checkm_result
[2023-06-19 08:40:40,801] [INFO] Task succeeded: CheckM
[2023-06-19 08:40:40,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:40:40,822] [INFO] ===== Completeness check finished =====
[2023-06-19 08:40:40,822] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:40:40,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018652385.1_ASM1865238v1_genomic.fna/markers.fasta)
[2023-06-19 08:40:40,822] [INFO] Task started: Blastn
[2023-06-19 08:40:40,822] [INFO] Running command: blastn -query GCA_018652385.1_ASM1865238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dec3792-00c5-49cc-a52d-b4f964de9689/dqc_reference/reference_markers_gtdb.fasta -out GCA_018652385.1_ASM1865238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:41,586] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:41,591] [INFO] Selected 23 target genomes.
[2023-06-19 08:40:41,591] [INFO] Target genome list was writen to GCA_018652385.1_ASM1865238v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:40:41,597] [INFO] Task started: fastANI
[2023-06-19 08:40:41,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg5695b601-2c83-468a-9871-68c93a521cca/GCA_018652385.1_ASM1865238v1_genomic.fna.gz --refList GCA_018652385.1_ASM1865238v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018652385.1_ASM1865238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:40:46,464] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:46,467] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:40:46,468] [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_018672055.1	s__JABHGM01 sp018672055	99.9798	222	222	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__UBA10009;g__JABHGM01	95.0	99.99	99.96	0.99	0.97	10	conclusive
--------------------------------------------------------------------------------
[2023-06-19 08:40:46,469] [INFO] GTDB search result was written to GCA_018652385.1_ASM1865238v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:40:46,470] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:40:46,472] [INFO] DFAST_QC result json was written to GCA_018652385.1_ASM1865238v1_genomic.fna/dqc_result.json
[2023-06-19 08:40:46,472] [INFO] DFAST_QC completed!
[2023-06-19 08:40:46,472] [INFO] Total running time: 0h0m28s