[2023-06-19 08:41:05,375] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:41:05,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:41:05,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference
[2023-06-19 08:41:06,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:41:06,558] [INFO] Task started: Prodigal
[2023-06-19 08:41:06,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg206a1a42-cf5e-4f91-b3e7-493be474a0ee/GCA_018677515.1_ASM1867751v1_genomic.fna.gz | prodigal -d GCA_018677515.1_ASM1867751v1_genomic.fna/cds.fna -a GCA_018677515.1_ASM1867751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:41:14,769] [INFO] Task succeeded: Prodigal
[2023-06-19 08:41:14,770] [INFO] Task started: HMMsearch
[2023-06-19 08:41:14,770] [INFO] Running command: hmmsearch --tblout GCA_018677515.1_ASM1867751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/reference_markers.hmm GCA_018677515.1_ASM1867751v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:41:14,969] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:41:14,971] [INFO] Found 6/6 markers.
[2023-06-19 08:41:14,998] [INFO] Query marker FASTA was written to GCA_018677515.1_ASM1867751v1_genomic.fna/markers.fasta
[2023-06-19 08:41:14,998] [INFO] Task started: Blastn
[2023-06-19 08:41:14,998] [INFO] Running command: blastn -query GCA_018677515.1_ASM1867751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/reference_markers.fasta -out GCA_018677515.1_ASM1867751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:41:15,707] [INFO] Task succeeded: Blastn
[2023-06-19 08:41:15,712] [INFO] Selected 31 target genomes.
[2023-06-19 08:41:15,712] [INFO] Target genome list was writen to GCA_018677515.1_ASM1867751v1_genomic.fna/target_genomes.txt
[2023-06-19 08:41:15,714] [INFO] Task started: fastANI
[2023-06-19 08:41:15,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg206a1a42-cf5e-4f91-b3e7-493be474a0ee/GCA_018677515.1_ASM1867751v1_genomic.fna.gz --refList GCA_018677515.1_ASM1867751v1_genomic.fna/target_genomes.txt --output GCA_018677515.1_ASM1867751v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:41:32,449] [INFO] Task succeeded: fastANI
[2023-06-19 08:41:32,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:41:32,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:41:32,452] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:41:32,452] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:41:32,452] [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 08:41:32,454] [INFO] DFAST Taxonomy check result was written to GCA_018677515.1_ASM1867751v1_genomic.fna/tc_result.tsv
[2023-06-19 08:41:32,455] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:41:32,455] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:41:32,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/checkm_data
[2023-06-19 08:41:32,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:41:32,489] [INFO] Task started: CheckM
[2023-06-19 08:41:32,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018677515.1_ASM1867751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018677515.1_ASM1867751v1_genomic.fna/checkm_input GCA_018677515.1_ASM1867751v1_genomic.fna/checkm_result
[2023-06-19 08:42:00,417] [INFO] Task succeeded: CheckM
[2023-06-19 08:42:00,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:42:00,439] [INFO] ===== Completeness check finished =====
[2023-06-19 08:42:00,439] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:42:00,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018677515.1_ASM1867751v1_genomic.fna/markers.fasta)
[2023-06-19 08:42:00,440] [INFO] Task started: Blastn
[2023-06-19 08:42:00,440] [INFO] Running command: blastn -query GCA_018677515.1_ASM1867751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg145ac48c-567d-43dd-8ada-66bc5924d3ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_018677515.1_ASM1867751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:42:01,693] [INFO] Task succeeded: Blastn
[2023-06-19 08:42:01,696] [INFO] Selected 27 target genomes.
[2023-06-19 08:42:01,696] [INFO] Target genome list was writen to GCA_018677515.1_ASM1867751v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:42:01,707] [INFO] Task started: fastANI
[2023-06-19 08:42:01,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg206a1a42-cf5e-4f91-b3e7-493be474a0ee/GCA_018677515.1_ASM1867751v1_genomic.fna.gz --refList GCA_018677515.1_ASM1867751v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018677515.1_ASM1867751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:42:15,819] [INFO] Task succeeded: fastANI
[2023-06-19 08:42:15,826] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:42:15,826] [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_013001885.1	s__JABDPF01 sp013001885	99.8318	902	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.83	99.83	0.95	0.93	4	conclusive
GCA_013042915.1	s__JABDPF01 sp013042915	77.5496	161	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDPF01	95.0	99.63	99.57	0.88	0.85	4	-
GCA_013042835.1	s__SZUA-36 sp013042835	77.4138	57	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__SZUA-36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011773845.1	s__WVWV01 sp011773845	76.8688	80	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__WVWV01	95.0	100.00	100.00	0.99	0.98	6	-
GCA_013002505.1	s__JABDJL01 sp013002505	76.1763	66	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__JABDJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008725655.1	s__W260 sp008725655	76.1737	80	944	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__W260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:42:15,828] [INFO] GTDB search result was written to GCA_018677515.1_ASM1867751v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:42:15,829] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:42:15,831] [INFO] DFAST_QC result json was written to GCA_018677515.1_ASM1867751v1_genomic.fna/dqc_result.json
[2023-06-19 08:42:15,831] [INFO] DFAST_QC completed!
[2023-06-19 08:42:15,831] [INFO] Total running time: 0h1m10s