[2023-06-19 15:07:05,480] [INFO] DFAST_QC pipeline started.
[2023-06-19 15:07:05,483] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 15:07:05,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference
[2023-06-19 15:07:07,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 15:07:07,264] [INFO] Task started: Prodigal
[2023-06-19 15:07:07,264] [INFO] Running command: gunzip -c /var/lib/cwl/stgcec561b3-08cd-434f-b39c-0ef4919e5553/GCA_018607665.1_ASM1860766v1_genomic.fna.gz | prodigal -d GCA_018607665.1_ASM1860766v1_genomic.fna/cds.fna -a GCA_018607665.1_ASM1860766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 15:07:15,334] [INFO] Task succeeded: Prodigal
[2023-06-19 15:07:15,335] [INFO] Task started: HMMsearch
[2023-06-19 15:07:15,335] [INFO] Running command: hmmsearch --tblout GCA_018607665.1_ASM1860766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/reference_markers.hmm GCA_018607665.1_ASM1860766v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 15:07:15,547] [INFO] Task succeeded: HMMsearch
[2023-06-19 15:07:15,548] [INFO] Found 6/6 markers.
[2023-06-19 15:07:15,576] [INFO] Query marker FASTA was written to GCA_018607665.1_ASM1860766v1_genomic.fna/markers.fasta
[2023-06-19 15:07:15,577] [INFO] Task started: Blastn
[2023-06-19 15:07:15,577] [INFO] Running command: blastn -query GCA_018607665.1_ASM1860766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/reference_markers.fasta -out GCA_018607665.1_ASM1860766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:07:16,204] [INFO] Task succeeded: Blastn
[2023-06-19 15:07:16,208] [INFO] Selected 26 target genomes.
[2023-06-19 15:07:16,208] [INFO] Target genome list was writen to GCA_018607665.1_ASM1860766v1_genomic.fna/target_genomes.txt
[2023-06-19 15:07:16,211] [INFO] Task started: fastANI
[2023-06-19 15:07:16,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec561b3-08cd-434f-b39c-0ef4919e5553/GCA_018607665.1_ASM1860766v1_genomic.fna.gz --refList GCA_018607665.1_ASM1860766v1_genomic.fna/target_genomes.txt --output GCA_018607665.1_ASM1860766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 15:07:30,412] [INFO] Task succeeded: fastANI
[2023-06-19 15:07:30,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 15:07:30,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 15:07:30,414] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 15:07:30,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 15:07:30,415] [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 15:07:30,416] [INFO] DFAST Taxonomy check result was written to GCA_018607665.1_ASM1860766v1_genomic.fna/tc_result.tsv
[2023-06-19 15:07:30,417] [INFO] ===== Taxonomy check completed =====
[2023-06-19 15:07:30,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 15:07:30,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/checkm_data
[2023-06-19 15:07:30,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 15:07:30,452] [INFO] Task started: CheckM
[2023-06-19 15:07:30,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607665.1_ASM1860766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607665.1_ASM1860766v1_genomic.fna/checkm_input GCA_018607665.1_ASM1860766v1_genomic.fna/checkm_result
[2023-06-19 15:07:59,327] [INFO] Task succeeded: CheckM
[2023-06-19 15:07:59,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 2.65%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 15:07:59,359] [INFO] ===== Completeness check finished =====
[2023-06-19 15:07:59,359] [INFO] ===== Start GTDB Search =====
[2023-06-19 15:07:59,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607665.1_ASM1860766v1_genomic.fna/markers.fasta)
[2023-06-19 15:07:59,359] [INFO] Task started: Blastn
[2023-06-19 15:07:59,360] [INFO] Running command: blastn -query GCA_018607665.1_ASM1860766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f55e74a-b431-4480-8ee7-542e052c662b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607665.1_ASM1860766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 15:08:00,354] [INFO] Task succeeded: Blastn
[2023-06-19 15:08:00,359] [INFO] Selected 15 target genomes.
[2023-06-19 15:08:00,359] [INFO] Target genome list was writen to GCA_018607665.1_ASM1860766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 15:08:00,360] [INFO] Task started: fastANI
[2023-06-19 15:08:00,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec561b3-08cd-434f-b39c-0ef4919e5553/GCA_018607665.1_ASM1860766v1_genomic.fna.gz --refList GCA_018607665.1_ASM1860766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607665.1_ASM1860766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 15:08:07,530] [INFO] Task succeeded: fastANI
[2023-06-19 15:08:07,535] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 15:08:07,535] [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_017854255.1	s__UBA9926 sp003451575	99.0082	884	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	conclusive
GCA_018645765.1	s__UBA9926 sp018645765	89.8702	484	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647445.1	s__UBA9926 sp018647445	86.1222	699	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	-
GCA_905182155.1	s__UBA9926 sp905182155	81.2345	467	976	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 15:08:07,538] [INFO] GTDB search result was written to GCA_018607665.1_ASM1860766v1_genomic.fna/result_gtdb.tsv
[2023-06-19 15:08:07,538] [INFO] ===== GTDB Search completed =====
[2023-06-19 15:08:07,540] [INFO] DFAST_QC result json was written to GCA_018607665.1_ASM1860766v1_genomic.fna/dqc_result.json
[2023-06-19 15:08:07,540] [INFO] DFAST_QC completed!
[2023-06-19 15:08:07,540] [INFO] Total running time: 0h1m2s