[2023-06-29 04:17:14,967] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:17:14,975] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:17:14,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference
[2023-06-29 04:17:16,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:17:16,162] [INFO] Task started: Prodigal
[2023-06-29 04:17:16,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg82ae708a-cf39-4847-8e78-15600efcb1a9/GCA_015487095.1_ASM1548709v1_genomic.fna.gz | prodigal -d GCA_015487095.1_ASM1548709v1_genomic.fna/cds.fna -a GCA_015487095.1_ASM1548709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:17:25,111] [INFO] Task succeeded: Prodigal
[2023-06-29 04:17:25,111] [INFO] Task started: HMMsearch
[2023-06-29 04:17:25,111] [INFO] Running command: hmmsearch --tblout GCA_015487095.1_ASM1548709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/reference_markers.hmm GCA_015487095.1_ASM1548709v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:17:25,310] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:17:25,311] [INFO] Found 6/6 markers.
[2023-06-29 04:17:25,340] [INFO] Query marker FASTA was written to GCA_015487095.1_ASM1548709v1_genomic.fna/markers.fasta
[2023-06-29 04:17:25,340] [INFO] Task started: Blastn
[2023-06-29 04:17:25,340] [INFO] Running command: blastn -query GCA_015487095.1_ASM1548709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/reference_markers.fasta -out GCA_015487095.1_ASM1548709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:17:25,935] [INFO] Task succeeded: Blastn
[2023-06-29 04:17:25,939] [INFO] Selected 28 target genomes.
[2023-06-29 04:17:25,940] [INFO] Target genome list was writen to GCA_015487095.1_ASM1548709v1_genomic.fna/target_genomes.txt
[2023-06-29 04:17:25,963] [INFO] Task started: fastANI
[2023-06-29 04:17:25,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg82ae708a-cf39-4847-8e78-15600efcb1a9/GCA_015487095.1_ASM1548709v1_genomic.fna.gz --refList GCA_015487095.1_ASM1548709v1_genomic.fna/target_genomes.txt --output GCA_015487095.1_ASM1548709v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:17:41,372] [INFO] Task succeeded: fastANI
[2023-06-29 04:17:41,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:17:41,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:17:41,374] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:17:41,375] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:17:41,375] [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
--------------------------------------------------------------------------------
[2023-06-29 04:17:41,377] [INFO] DFAST Taxonomy check result was written to GCA_015487095.1_ASM1548709v1_genomic.fna/tc_result.tsv
[2023-06-29 04:17:41,378] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:17:41,378] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:17:41,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/checkm_data
[2023-06-29 04:17:41,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:17:41,418] [INFO] Task started: CheckM
[2023-06-29 04:17:41,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015487095.1_ASM1548709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015487095.1_ASM1548709v1_genomic.fna/checkm_input GCA_015487095.1_ASM1548709v1_genomic.fna/checkm_result
[2023-06-29 04:18:12,587] [INFO] Task succeeded: CheckM
[2023-06-29 04:18:12,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 04:18:12,602] [INFO] ===== Completeness check finished =====
[2023-06-29 04:18:12,602] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:18:12,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015487095.1_ASM1548709v1_genomic.fna/markers.fasta)
[2023-06-29 04:18:12,603] [INFO] Task started: Blastn
[2023-06-29 04:18:12,603] [INFO] Running command: blastn -query GCA_015487095.1_ASM1548709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366813d5-0912-4415-9b1e-26d15e0f295c/dqc_reference/reference_markers_gtdb.fasta -out GCA_015487095.1_ASM1548709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:18:13,448] [INFO] Task succeeded: Blastn
[2023-06-29 04:18:13,453] [INFO] Selected 11 target genomes.
[2023-06-29 04:18:13,453] [INFO] Target genome list was writen to GCA_015487095.1_ASM1548709v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:18:13,456] [INFO] Task started: fastANI
[2023-06-29 04:18:13,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg82ae708a-cf39-4847-8e78-15600efcb1a9/GCA_015487095.1_ASM1548709v1_genomic.fna.gz --refList GCA_015487095.1_ASM1548709v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015487095.1_ASM1548709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:18:22,037] [INFO] Task succeeded: fastANI
[2023-06-29 04:18:22,045] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:18:22,046] [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_015487095.1	s__SZUA-152 sp015487095	100.0	1007	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	98.98	98.98	0.85	0.85	2	conclusive
GCA_003229995.1	s__SZUA-152 sp003229995	86.5406	415	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151355.1	s__SZUA-152 sp013151355	83.6717	562	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321815.1	s__SZUA-152 sp011321815	83.2531	690	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	97.33	97.33	0.90	0.90	2	-
GCA_013151575.1	s__JAADHZ01 sp013151575	78.0173	158	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__JAADHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051685.1	s__SZUA-152 sp011051685	77.3768	203	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401775.2	s__SZUA-152 sp002401775	77.3356	195	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.6714	52	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-29 04:18:22,047] [INFO] GTDB search result was written to GCA_015487095.1_ASM1548709v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:18:22,048] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:18:22,050] [INFO] DFAST_QC result json was written to GCA_015487095.1_ASM1548709v1_genomic.fna/dqc_result.json
[2023-06-29 04:18:22,050] [INFO] DFAST_QC completed!
[2023-06-29 04:18:22,050] [INFO] Total running time: 0h1m7s