[2023-06-28 12:00:31,416] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:00:31,421] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:00:31,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference
[2023-06-28 12:00:32,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:00:32,681] [INFO] Task started: Prodigal
[2023-06-28 12:00:32,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b53aa1e-45fa-422e-a719-39f2cc68c114/GCA_027409655.1_ASM2740965v1_genomic.fna.gz | prodigal -d GCA_027409655.1_ASM2740965v1_genomic.fna/cds.fna -a GCA_027409655.1_ASM2740965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:00:38,717] [INFO] Task succeeded: Prodigal
[2023-06-28 12:00:38,717] [INFO] Task started: HMMsearch
[2023-06-28 12:00:38,717] [INFO] Running command: hmmsearch --tblout GCA_027409655.1_ASM2740965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/reference_markers.hmm GCA_027409655.1_ASM2740965v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:00:38,964] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:00:38,966] [INFO] Found 6/6 markers.
[2023-06-28 12:00:39,000] [INFO] Query marker FASTA was written to GCA_027409655.1_ASM2740965v1_genomic.fna/markers.fasta
[2023-06-28 12:00:39,000] [INFO] Task started: Blastn
[2023-06-28 12:00:39,000] [INFO] Running command: blastn -query GCA_027409655.1_ASM2740965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/reference_markers.fasta -out GCA_027409655.1_ASM2740965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:00:39,636] [INFO] Task succeeded: Blastn
[2023-06-28 12:00:39,640] [INFO] Selected 22 target genomes.
[2023-06-28 12:00:39,640] [INFO] Target genome list was writen to GCA_027409655.1_ASM2740965v1_genomic.fna/target_genomes.txt
[2023-06-28 12:00:39,763] [INFO] Task started: fastANI
[2023-06-28 12:00:39,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b53aa1e-45fa-422e-a719-39f2cc68c114/GCA_027409655.1_ASM2740965v1_genomic.fna.gz --refList GCA_027409655.1_ASM2740965v1_genomic.fna/target_genomes.txt --output GCA_027409655.1_ASM2740965v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:00:56,416] [INFO] Task succeeded: fastANI
[2023-06-28 12:00:56,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:00:56,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:00:56,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:00:56,419] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:00:56,419] [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 12:00:56,422] [INFO] DFAST Taxonomy check result was written to GCA_027409655.1_ASM2740965v1_genomic.fna/tc_result.tsv
[2023-06-28 12:00:56,423] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:00:56,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:00:56,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/checkm_data
[2023-06-28 12:00:56,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:00:56,458] [INFO] Task started: CheckM
[2023-06-28 12:00:56,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027409655.1_ASM2740965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027409655.1_ASM2740965v1_genomic.fna/checkm_input GCA_027409655.1_ASM2740965v1_genomic.fna/checkm_result
[2023-06-28 12:01:21,502] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:21,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:21,529] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:21,530] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:21,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027409655.1_ASM2740965v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:21,531] [INFO] Task started: Blastn
[2023-06-28 12:01:21,532] [INFO] Running command: blastn -query GCA_027409655.1_ASM2740965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5427ee6-e23a-4b89-bf2f-6a916090a8a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_027409655.1_ASM2740965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:22,402] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:22,405] [INFO] Selected 23 target genomes.
[2023-06-28 12:01:22,406] [INFO] Target genome list was writen to GCA_027409655.1_ASM2740965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:22,433] [INFO] Task started: fastANI
[2023-06-28 12:01:22,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b53aa1e-45fa-422e-a719-39f2cc68c114/GCA_027409655.1_ASM2740965v1_genomic.fna.gz --refList GCA_027409655.1_ASM2740965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027409655.1_ASM2740965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:34,440] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:34,445] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:01:34,445] [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_013044385.1	s__JABEUN01 sp013044385	96.544	692	748	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__JABEUN01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-28 12:01:34,448] [INFO] GTDB search result was written to GCA_027409655.1_ASM2740965v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:34,448] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:34,451] [INFO] DFAST_QC result json was written to GCA_027409655.1_ASM2740965v1_genomic.fna/dqc_result.json
[2023-06-28 12:01:34,451] [INFO] DFAST_QC completed!
[2023-06-28 12:01:34,452] [INFO] Total running time: 0h1m3s