[2023-06-28 06:09:43,392] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:09:43,395] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:09:43,395] [INFO] DQC Reference Directory: /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference
[2023-06-28 06:09:45,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:09:45,992] [INFO] Task started: Prodigal
[2023-06-28 06:09:45,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgea2638d9-6788-499b-9160-3cc5184b5660/GCA_017392845.1_ASM1739284v1_genomic.fna.gz | prodigal -d GCA_017392845.1_ASM1739284v1_genomic.fna/cds.fna -a GCA_017392845.1_ASM1739284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:09:49,183] [INFO] Task succeeded: Prodigal
[2023-06-28 06:09:49,184] [INFO] Task started: HMMsearch
[2023-06-28 06:09:49,184] [INFO] Running command: hmmsearch --tblout GCA_017392845.1_ASM1739284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/reference_markers.hmm GCA_017392845.1_ASM1739284v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:09:49,420] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:09:49,422] [INFO] Found 6/6 markers.
[2023-06-28 06:09:49,445] [INFO] Query marker FASTA was written to GCA_017392845.1_ASM1739284v1_genomic.fna/markers.fasta
[2023-06-28 06:09:49,445] [INFO] Task started: Blastn
[2023-06-28 06:09:49,445] [INFO] Running command: blastn -query GCA_017392845.1_ASM1739284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/reference_markers.fasta -out GCA_017392845.1_ASM1739284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:09:50,084] [INFO] Task succeeded: Blastn
[2023-06-28 06:09:50,088] [INFO] Selected 9 target genomes.
[2023-06-28 06:09:50,088] [INFO] Target genome list was writen to GCA_017392845.1_ASM1739284v1_genomic.fna/target_genomes.txt
[2023-06-28 06:09:50,121] [INFO] Task started: fastANI
[2023-06-28 06:09:50,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgea2638d9-6788-499b-9160-3cc5184b5660/GCA_017392845.1_ASM1739284v1_genomic.fna.gz --refList GCA_017392845.1_ASM1739284v1_genomic.fna/target_genomes.txt --output GCA_017392845.1_ASM1739284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:09:57,403] [INFO] Task succeeded: fastANI
[2023-06-28 06:09:57,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:09:57,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:09:57,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:09:57,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 06:09:57,406] [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
--------------------------------------------------------------------------------
[2023-06-28 06:09:57,408] [INFO] DFAST Taxonomy check result was written to GCA_017392845.1_ASM1739284v1_genomic.fna/tc_result.tsv
[2023-06-28 06:09:57,409] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:09:57,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:09:57,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/checkm_data
[2023-06-28 06:09:57,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:09:57,433] [INFO] Task started: CheckM
[2023-06-28 06:09:57,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017392845.1_ASM1739284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017392845.1_ASM1739284v1_genomic.fna/checkm_input GCA_017392845.1_ASM1739284v1_genomic.fna/checkm_result
[2023-06-28 06:10:17,286] [INFO] Task succeeded: CheckM
[2023-06-28 06:10:17,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:10:17,325] [INFO] ===== Completeness check finished =====
[2023-06-28 06:10:17,325] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:10:17,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017392845.1_ASM1739284v1_genomic.fna/markers.fasta)
[2023-06-28 06:10:17,326] [INFO] Task started: Blastn
[2023-06-28 06:10:17,326] [INFO] Running command: blastn -query GCA_017392845.1_ASM1739284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge11e8213-236d-4fde-bbb6-471539d3d648/dqc_reference/reference_markers_gtdb.fasta -out GCA_017392845.1_ASM1739284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:18,302] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:18,309] [INFO] Selected 21 target genomes.
[2023-06-28 06:10:18,309] [INFO] Target genome list was writen to GCA_017392845.1_ASM1739284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:10:18,369] [INFO] Task started: fastANI
[2023-06-28 06:10:18,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgea2638d9-6788-499b-9160-3cc5184b5660/GCA_017392845.1_ASM1739284v1_genomic.fna.gz --refList GCA_017392845.1_ASM1739284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017392845.1_ASM1739284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:10:27,091] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:27,098] [INFO] Found 2 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 06:10:27,098] [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_902802045.1	s__Limivicinus sp902802045	98.344	375	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.63	95.09	0.97	0.95	5	inconclusive
GCA_017430455.1	s__Limivicinus sp017430455	95.0799	370	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.47	0.95	0.95	2	inconclusive
--------------------------------------------------------------------------------
[2023-06-28 06:10:27,101] [INFO] GTDB search result was written to GCA_017392845.1_ASM1739284v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:10:27,102] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:10:27,105] [INFO] DFAST_QC result json was written to GCA_017392845.1_ASM1739284v1_genomic.fna/dqc_result.json
[2023-06-28 06:10:27,106] [INFO] DFAST_QC completed!
[2023-06-28 06:10:27,106] [INFO] Total running time: 0h0m44s