[2023-06-29 16:18:34,404] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:18:34,407] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:18:34,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference
[2023-06-29 16:18:35,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:18:35,631] [INFO] Task started: Prodigal
[2023-06-29 16:18:35,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgd07f7df4-ed8d-4bf3-9c2a-2d3272f7ea15/GCA_021735245.1_ASM2173524v1_genomic.fna.gz | prodigal -d GCA_021735245.1_ASM2173524v1_genomic.fna/cds.fna -a GCA_021735245.1_ASM2173524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:18:39,288] [INFO] Task succeeded: Prodigal
[2023-06-29 16:18:39,288] [INFO] Task started: HMMsearch
[2023-06-29 16:18:39,288] [INFO] Running command: hmmsearch --tblout GCA_021735245.1_ASM2173524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/reference_markers.hmm GCA_021735245.1_ASM2173524v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:18:39,546] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:18:39,547] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd07f7df4-ed8d-4bf3-9c2a-2d3272f7ea15/GCA_021735245.1_ASM2173524v1_genomic.fna.gz]
[2023-06-29 16:18:39,572] [INFO] Query marker FASTA was written to GCA_021735245.1_ASM2173524v1_genomic.fna/markers.fasta
[2023-06-29 16:18:39,573] [INFO] Task started: Blastn
[2023-06-29 16:18:39,573] [INFO] Running command: blastn -query GCA_021735245.1_ASM2173524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/reference_markers.fasta -out GCA_021735245.1_ASM2173524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:18:40,144] [INFO] Task succeeded: Blastn
[2023-06-29 16:18:40,148] [INFO] Selected 13 target genomes.
[2023-06-29 16:18:40,148] [INFO] Target genome list was writen to GCA_021735245.1_ASM2173524v1_genomic.fna/target_genomes.txt
[2023-06-29 16:18:40,162] [INFO] Task started: fastANI
[2023-06-29 16:18:40,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07f7df4-ed8d-4bf3-9c2a-2d3272f7ea15/GCA_021735245.1_ASM2173524v1_genomic.fna.gz --refList GCA_021735245.1_ASM2173524v1_genomic.fna/target_genomes.txt --output GCA_021735245.1_ASM2173524v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:18:48,850] [INFO] Task succeeded: fastANI
[2023-06-29 16:18:48,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:18:48,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:18:48,853] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:18:48,853] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:18:48,853] [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 16:18:48,855] [INFO] DFAST Taxonomy check result was written to GCA_021735245.1_ASM2173524v1_genomic.fna/tc_result.tsv
[2023-06-29 16:18:48,856] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:18:48,856] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:18:48,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/checkm_data
[2023-06-29 16:18:48,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:18:48,897] [INFO] Task started: CheckM
[2023-06-29 16:18:48,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021735245.1_ASM2173524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021735245.1_ASM2173524v1_genomic.fna/checkm_input GCA_021735245.1_ASM2173524v1_genomic.fna/checkm_result
[2023-06-29 16:19:07,914] [INFO] Task succeeded: CheckM
[2023-06-29 16:19:07,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:19:07,937] [INFO] ===== Completeness check finished =====
[2023-06-29 16:19:07,938] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:19:07,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021735245.1_ASM2173524v1_genomic.fna/markers.fasta)
[2023-06-29 16:19:07,938] [INFO] Task started: Blastn
[2023-06-29 16:19:07,939] [INFO] Running command: blastn -query GCA_021735245.1_ASM2173524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd63ff2e4-06ba-4628-99da-449fb0cfb16e/dqc_reference/reference_markers_gtdb.fasta -out GCA_021735245.1_ASM2173524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:08,713] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:08,718] [INFO] Selected 10 target genomes.
[2023-06-29 16:19:08,718] [INFO] Target genome list was writen to GCA_021735245.1_ASM2173524v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:19:08,766] [INFO] Task started: fastANI
[2023-06-29 16:19:08,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07f7df4-ed8d-4bf3-9c2a-2d3272f7ea15/GCA_021735245.1_ASM2173524v1_genomic.fna.gz --refList GCA_021735245.1_ASM2173524v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021735245.1_ASM2173524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:19:14,450] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:14,454] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:19:14,454] [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_018335015.1	s__JAGXLP01 sp018335015	82.6294	295	602	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	99.44	99.44	0.87	0.87	2	-
GCA_018334915.1	s__JAGXLP01 sp018334915	81.154	278	602	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:19:14,456] [INFO] GTDB search result was written to GCA_021735245.1_ASM2173524v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:19:14,457] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:19:14,459] [INFO] DFAST_QC result json was written to GCA_021735245.1_ASM2173524v1_genomic.fna/dqc_result.json
[2023-06-29 16:19:14,459] [INFO] DFAST_QC completed!
[2023-06-29 16:19:14,459] [INFO] Total running time: 0h0m40s