[2023-06-18 20:10:11,049] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:10:11,051] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:10:11,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference
[2023-06-18 20:10:12,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:10:12,229] [INFO] Task started: Prodigal
[2023-06-18 20:10:12,229] [INFO] Running command: gunzip -c /var/lib/cwl/stga7bd423b-6668-4f2f-99e9-d6bd95b4cdd8/GCA_018653205.1_ASM1865320v1_genomic.fna.gz | prodigal -d GCA_018653205.1_ASM1865320v1_genomic.fna/cds.fna -a GCA_018653205.1_ASM1865320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:10:16,800] [INFO] Task succeeded: Prodigal
[2023-06-18 20:10:16,800] [INFO] Task started: HMMsearch
[2023-06-18 20:10:16,801] [INFO] Running command: hmmsearch --tblout GCA_018653205.1_ASM1865320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/reference_markers.hmm GCA_018653205.1_ASM1865320v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:10:17,021] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:10:17,022] [INFO] Found 6/6 markers.
[2023-06-18 20:10:17,048] [INFO] Query marker FASTA was written to GCA_018653205.1_ASM1865320v1_genomic.fna/markers.fasta
[2023-06-18 20:10:17,048] [INFO] Task started: Blastn
[2023-06-18 20:10:17,048] [INFO] Running command: blastn -query GCA_018653205.1_ASM1865320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/reference_markers.fasta -out GCA_018653205.1_ASM1865320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:17,673] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:17,678] [INFO] Selected 21 target genomes.
[2023-06-18 20:10:17,679] [INFO] Target genome list was writen to GCA_018653205.1_ASM1865320v1_genomic.fna/target_genomes.txt
[2023-06-18 20:10:17,684] [INFO] Task started: fastANI
[2023-06-18 20:10:17,684] [INFO] Running command: fastANI --query /var/lib/cwl/stga7bd423b-6668-4f2f-99e9-d6bd95b4cdd8/GCA_018653205.1_ASM1865320v1_genomic.fna.gz --refList GCA_018653205.1_ASM1865320v1_genomic.fna/target_genomes.txt --output GCA_018653205.1_ASM1865320v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:10:27,167] [INFO] Task succeeded: fastANI
[2023-06-18 20:10:27,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:10:27,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:10:27,170] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:10:27,170] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:10:27,171] [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
--------------------------------------------------------------------------------
[2023-06-18 20:10:27,173] [INFO] DFAST Taxonomy check result was written to GCA_018653205.1_ASM1865320v1_genomic.fna/tc_result.tsv
[2023-06-18 20:10:27,174] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:10:27,174] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:10:27,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/checkm_data
[2023-06-18 20:10:27,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:10:27,206] [INFO] Task started: CheckM
[2023-06-18 20:10:27,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018653205.1_ASM1865320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018653205.1_ASM1865320v1_genomic.fna/checkm_input GCA_018653205.1_ASM1865320v1_genomic.fna/checkm_result
[2023-06-18 20:10:48,551] [INFO] Task succeeded: CheckM
[2023-06-18 20:10:48,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.98%
Contamintation: 1.39%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 20:10:48,576] [INFO] ===== Completeness check finished =====
[2023-06-18 20:10:48,577] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:10:48,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018653205.1_ASM1865320v1_genomic.fna/markers.fasta)
[2023-06-18 20:10:48,577] [INFO] Task started: Blastn
[2023-06-18 20:10:48,577] [INFO] Running command: blastn -query GCA_018653205.1_ASM1865320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41739bd7-2ca0-439a-9e3a-6dcf15fb088d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018653205.1_ASM1865320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:49,535] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:49,540] [INFO] Selected 14 target genomes.
[2023-06-18 20:10:49,541] [INFO] Target genome list was writen to GCA_018653205.1_ASM1865320v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:10:49,548] [INFO] Task started: fastANI
[2023-06-18 20:10:49,548] [INFO] Running command: fastANI --query /var/lib/cwl/stga7bd423b-6668-4f2f-99e9-d6bd95b4cdd8/GCA_018653205.1_ASM1865320v1_genomic.fna.gz --refList GCA_018653205.1_ASM1865320v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018653205.1_ASM1865320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:10:54,396] [INFO] Task succeeded: fastANI
[2023-06-18 20:10:54,402] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:10:54,402] [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_018672825.1	s__UBA868 sp018672825	99.4595	519	562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.43	99.28	0.91	0.86	14	conclusive
GCA_004212795.1	s__UBA868 sp002295285	91.9831	438	562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.27	99.27	0.84	0.84	2	-
GCA_016776875.1	s__UBA868 sp016776875	91.2409	356	562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:10:54,404] [INFO] GTDB search result was written to GCA_018653205.1_ASM1865320v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:10:54,405] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:10:54,407] [INFO] DFAST_QC result json was written to GCA_018653205.1_ASM1865320v1_genomic.fna/dqc_result.json
[2023-06-18 20:10:54,407] [INFO] DFAST_QC completed!
[2023-06-18 20:10:54,407] [INFO] Total running time: 0h0m43s