[2024-01-25 17:40:51,015] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:51,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:51,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference
[2024-01-25 17:40:52,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:52,152] [INFO] Task started: Prodigal
[2024-01-25 17:40:52,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg31c92939-ac4d-4b9e-a860-a00b842baf0e/GCF_019008365.1_ASM1900836v1_genomic.fna.gz | prodigal -d GCF_019008365.1_ASM1900836v1_genomic.fna/cds.fna -a GCF_019008365.1_ASM1900836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:00,556] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:00,556] [INFO] Task started: HMMsearch
[2024-01-25 17:41:00,556] [INFO] Running command: hmmsearch --tblout GCF_019008365.1_ASM1900836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/reference_markers.hmm GCF_019008365.1_ASM1900836v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:00,786] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:00,787] [INFO] Found 6/6 markers.
[2024-01-25 17:41:00,819] [INFO] Query marker FASTA was written to GCF_019008365.1_ASM1900836v1_genomic.fna/markers.fasta
[2024-01-25 17:41:00,819] [INFO] Task started: Blastn
[2024-01-25 17:41:00,819] [INFO] Running command: blastn -query GCF_019008365.1_ASM1900836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/reference_markers.fasta -out GCF_019008365.1_ASM1900836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:01,344] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:01,347] [INFO] Selected 16 target genomes.
[2024-01-25 17:41:01,348] [INFO] Target genome list was writen to GCF_019008365.1_ASM1900836v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:01,363] [INFO] Task started: fastANI
[2024-01-25 17:41:01,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c92939-ac4d-4b9e-a860-a00b842baf0e/GCF_019008365.1_ASM1900836v1_genomic.fna.gz --refList GCF_019008365.1_ASM1900836v1_genomic.fna/target_genomes.txt --output GCF_019008365.1_ASM1900836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:12,910] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:12,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:12,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:12,914] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:12,914] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:12,914] [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
Phosphitispora fastidiosa	strain=DYL19	GCA_019008365.1	2837202	2837202	type	True	100.0	1314	1317	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:41:12,916] [INFO] DFAST Taxonomy check result was written to GCF_019008365.1_ASM1900836v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:12,916] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:12,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:12,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/checkm_data
[2024-01-25 17:41:12,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:12,958] [INFO] Task started: CheckM
[2024-01-25 17:41:12,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019008365.1_ASM1900836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019008365.1_ASM1900836v1_genomic.fna/checkm_input GCF_019008365.1_ASM1900836v1_genomic.fna/checkm_result
[2024-01-25 17:41:41,548] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:41,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:41,569] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:41,569] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:41,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019008365.1_ASM1900836v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:41,570] [INFO] Task started: Blastn
[2024-01-25 17:41:41,570] [INFO] Running command: blastn -query GCF_019008365.1_ASM1900836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fcec36a-5a37-43e4-8072-35633d4daa3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019008365.1_ASM1900836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:42,361] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:42,363] [INFO] Selected 12 target genomes.
[2024-01-25 17:41:42,363] [INFO] Target genome list was writen to GCF_019008365.1_ASM1900836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:42,377] [INFO] Task started: fastANI
[2024-01-25 17:41:42,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c92939-ac4d-4b9e-a860-a00b842baf0e/GCF_019008365.1_ASM1900836v1_genomic.fna.gz --refList GCF_019008365.1_ASM1900836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019008365.1_ASM1900836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:49,767] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:49,772] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:49,772] [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_019008365.1	s__DYL19 sp019008365	100.0	1314	1317	d__Bacteria;p__Firmicutes_B;c__Thermincolia;o__Thermincolales;f__UBA2595;g__DYL19	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016841725.1	s__DYL19 sp016841725	91.2529	981	1317	d__Bacteria;p__Firmicutes_B;c__Thermincolia;o__Thermincolales;f__UBA2595;g__DYL19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841325.1	s__DYL19 sp016841325	82.8369	810	1317	d__Bacteria;p__Firmicutes_B;c__Thermincolia;o__Thermincolales;f__UBA2595;g__DYL19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840275.1	s__W-Firmicutes-14 sp002840275	77.6101	195	1317	d__Bacteria;p__Firmicutes_B;c__Thermincolia;o__Thermincolales;f__UBA2595;g__W-Firmicutes-14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:49,774] [INFO] GTDB search result was written to GCF_019008365.1_ASM1900836v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:49,775] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:49,777] [INFO] DFAST_QC result json was written to GCF_019008365.1_ASM1900836v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:49,777] [INFO] DFAST_QC completed!
[2024-01-25 17:41:49,778] [INFO] Total running time: 0h0m59s