[2023-06-04 20:24:38,517] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:24:38,525] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:24:38,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference
[2023-06-04 20:24:40,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:24:40,742] [INFO] Task started: Prodigal
[2023-06-04 20:24:40,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ab872ca-9f19-43e0-87ea-c96fdeb90fec/GCA_001792575.1_ASM179257v1_genomic.fna.gz | prodigal -d GCA_001792575.1_ASM179257v1_genomic.fna/cds.fna -a GCA_001792575.1_ASM179257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:44,213] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:44,213] [INFO] Task started: HMMsearch
[2023-06-04 20:24:44,214] [INFO] Running command: hmmsearch --tblout GCA_001792575.1_ASM179257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/reference_markers.hmm GCA_001792575.1_ASM179257v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:44,435] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:44,437] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ab872ca-9f19-43e0-87ea-c96fdeb90fec/GCA_001792575.1_ASM179257v1_genomic.fna.gz]
[2023-06-04 20:24:44,453] [INFO] Query marker FASTA was written to GCA_001792575.1_ASM179257v1_genomic.fna/markers.fasta
[2023-06-04 20:24:44,454] [INFO] Task started: Blastn
[2023-06-04 20:24:44,454] [INFO] Running command: blastn -query GCA_001792575.1_ASM179257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/reference_markers.fasta -out GCA_001792575.1_ASM179257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:45,012] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:45,017] [INFO] Selected 10 target genomes.
[2023-06-04 20:24:45,017] [INFO] Target genome list was writen to GCA_001792575.1_ASM179257v1_genomic.fna/target_genomes.txt
[2023-06-04 20:24:45,021] [INFO] Task started: fastANI
[2023-06-04 20:24:45,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab872ca-9f19-43e0-87ea-c96fdeb90fec/GCA_001792575.1_ASM179257v1_genomic.fna.gz --refList GCA_001792575.1_ASM179257v1_genomic.fna/target_genomes.txt --output GCA_001792575.1_ASM179257v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:50,766] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:50,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:50,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:50,770] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:50,770] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:24:50,770] [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
--------------------------------------------------------------------------------
[2023-06-04 20:24:50,773] [INFO] DFAST Taxonomy check result was written to GCA_001792575.1_ASM179257v1_genomic.fna/tc_result.tsv
[2023-06-04 20:24:50,774] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:50,775] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:50,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/checkm_data
[2023-06-04 20:24:50,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:50,801] [INFO] Task started: CheckM
[2023-06-04 20:24:50,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001792575.1_ASM179257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001792575.1_ASM179257v1_genomic.fna/checkm_input GCA_001792575.1_ASM179257v1_genomic.fna/checkm_result
[2023-06-04 20:25:08,490] [INFO] Task succeeded: CheckM
[2023-06-04 20:25:08,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:25:08,514] [INFO] ===== Completeness check finished =====
[2023-06-04 20:25:08,515] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:25:08,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001792575.1_ASM179257v1_genomic.fna/markers.fasta)
[2023-06-04 20:25:08,515] [INFO] Task started: Blastn
[2023-06-04 20:25:08,516] [INFO] Running command: blastn -query GCA_001792575.1_ASM179257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f986b1c-ebab-473f-b72d-cf99f2a16bdf/dqc_reference/reference_markers_gtdb.fasta -out GCA_001792575.1_ASM179257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:25:09,270] [INFO] Task succeeded: Blastn
[2023-06-04 20:25:09,277] [INFO] Selected 13 target genomes.
[2023-06-04 20:25:09,277] [INFO] Target genome list was writen to GCA_001792575.1_ASM179257v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:25:09,292] [INFO] Task started: fastANI
[2023-06-04 20:25:09,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab872ca-9f19-43e0-87ea-c96fdeb90fec/GCA_001792575.1_ASM179257v1_genomic.fna.gz --refList GCA_001792575.1_ASM179257v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001792575.1_ASM179257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:25:14,519] [INFO] Task succeeded: fastANI
[2023-06-04 20:25:14,524] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:25:14,525] [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_001793095.1	s__HO2-FULL-38-9 sp001793095	99.9426	324	328	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__GWA2-44-7;f__UBA8517;g__HO2-FULL-38-9	95.0	99.97	99.94	0.99	0.97	4	conclusive
--------------------------------------------------------------------------------
[2023-06-04 20:25:14,527] [INFO] GTDB search result was written to GCA_001792575.1_ASM179257v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:25:14,529] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:25:14,532] [INFO] DFAST_QC result json was written to GCA_001792575.1_ASM179257v1_genomic.fna/dqc_result.json
[2023-06-04 20:25:14,532] [INFO] DFAST_QC completed!
[2023-06-04 20:25:14,533] [INFO] Total running time: 0h0m36s