[2023-06-18 21:21:11,998] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:21:12,000] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:21:12,000] [INFO] DQC Reference Directory: /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference
[2023-06-18 21:21:15,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:21:15,023] [INFO] Task started: Prodigal
[2023-06-18 21:21:15,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg07b1a953-f4fb-49a2-ba10-0c25908ade60/GCA_018676415.1_ASM1867641v1_genomic.fna.gz | prodigal -d GCA_018676415.1_ASM1867641v1_genomic.fna/cds.fna -a GCA_018676415.1_ASM1867641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:21:25,379] [INFO] Task succeeded: Prodigal
[2023-06-18 21:21:25,379] [INFO] Task started: HMMsearch
[2023-06-18 21:21:25,380] [INFO] Running command: hmmsearch --tblout GCA_018676415.1_ASM1867641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/reference_markers.hmm GCA_018676415.1_ASM1867641v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:21:25,733] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:21:25,734] [INFO] Found 6/6 markers.
[2023-06-18 21:21:25,783] [INFO] Query marker FASTA was written to GCA_018676415.1_ASM1867641v1_genomic.fna/markers.fasta
[2023-06-18 21:21:25,784] [INFO] Task started: Blastn
[2023-06-18 21:21:25,784] [INFO] Running command: blastn -query GCA_018676415.1_ASM1867641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/reference_markers.fasta -out GCA_018676415.1_ASM1867641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:26,371] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:26,378] [INFO] Selected 16 target genomes.
[2023-06-18 21:21:26,379] [INFO] Target genome list was writen to GCA_018676415.1_ASM1867641v1_genomic.fna/target_genomes.txt
[2023-06-18 21:21:26,382] [INFO] Task started: fastANI
[2023-06-18 21:21:26,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b1a953-f4fb-49a2-ba10-0c25908ade60/GCA_018676415.1_ASM1867641v1_genomic.fna.gz --refList GCA_018676415.1_ASM1867641v1_genomic.fna/target_genomes.txt --output GCA_018676415.1_ASM1867641v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:21:36,575] [INFO] Task succeeded: fastANI
[2023-06-18 21:21:36,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:21:36,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:21:36,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:21:36,578] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:21:36,578] [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
--------------------------------------------------------------------------------
[2023-06-18 21:21:36,583] [INFO] DFAST Taxonomy check result was written to GCA_018676415.1_ASM1867641v1_genomic.fna/tc_result.tsv
[2023-06-18 21:21:36,584] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:21:36,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:21:36,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/checkm_data
[2023-06-18 21:21:36,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:21:36,644] [INFO] Task started: CheckM
[2023-06-18 21:21:36,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018676415.1_ASM1867641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018676415.1_ASM1867641v1_genomic.fna/checkm_input GCA_018676415.1_ASM1867641v1_genomic.fna/checkm_result
[2023-06-18 21:22:14,077] [INFO] Task succeeded: CheckM
[2023-06-18 21:22:14,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:22:14,107] [INFO] ===== Completeness check finished =====
[2023-06-18 21:22:14,107] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:22:14,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018676415.1_ASM1867641v1_genomic.fna/markers.fasta)
[2023-06-18 21:22:14,108] [INFO] Task started: Blastn
[2023-06-18 21:22:14,108] [INFO] Running command: blastn -query GCA_018676415.1_ASM1867641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ab153c-411d-4501-96d4-3436e3823976/dqc_reference/reference_markers_gtdb.fasta -out GCA_018676415.1_ASM1867641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:22:14,842] [INFO] Task succeeded: Blastn
[2023-06-18 21:22:14,849] [INFO] Selected 21 target genomes.
[2023-06-18 21:22:14,850] [INFO] Target genome list was writen to GCA_018676415.1_ASM1867641v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:22:14,903] [INFO] Task started: fastANI
[2023-06-18 21:22:14,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b1a953-f4fb-49a2-ba10-0c25908ade60/GCA_018676415.1_ASM1867641v1_genomic.fna.gz --refList GCA_018676415.1_ASM1867641v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018676415.1_ASM1867641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:22:26,195] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:26,200] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:22:26,200] [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_018644935.1	s__JABGPL01 sp018644935	99.5027	1168	1395	d__Bacteria;p__AABM5-125-24;c__AABM5-125-24;o__AABM5-125-24;f__AABM5-125-24;g__JABGPL01	95.0	99.50	99.49	0.82	0.81	3	conclusive
--------------------------------------------------------------------------------
[2023-06-18 21:22:26,202] [INFO] GTDB search result was written to GCA_018676415.1_ASM1867641v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:22:26,207] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:22:26,211] [INFO] DFAST_QC result json was written to GCA_018676415.1_ASM1867641v1_genomic.fna/dqc_result.json
[2023-06-18 21:22:26,212] [INFO] DFAST_QC completed!
[2023-06-18 21:22:26,212] [INFO] Total running time: 0h1m14s