[2024-01-24 14:19:59,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference
[2024-01-24 14:20:00,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:00,910] [INFO] Task started: Prodigal
[2024-01-24 14:20:00,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg31223f46-7f7a-43e9-8ec1-71533ce24e07/GCF_031598375.1_ASM3159837v1_genomic.fna.gz | prodigal -d GCF_031598375.1_ASM3159837v1_genomic.fna/cds.fna -a GCF_031598375.1_ASM3159837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:08,815] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:08,816] [INFO] Task started: HMMsearch
[2024-01-24 14:20:08,816] [INFO] Running command: hmmsearch --tblout GCF_031598375.1_ASM3159837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/reference_markers.hmm GCF_031598375.1_ASM3159837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:09,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:09,106] [INFO] Found 6/6 markers.
[2024-01-24 14:20:09,144] [INFO] Query marker FASTA was written to GCF_031598375.1_ASM3159837v1_genomic.fna/markers.fasta
[2024-01-24 14:20:09,145] [INFO] Task started: Blastn
[2024-01-24 14:20:09,145] [INFO] Running command: blastn -query GCF_031598375.1_ASM3159837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/reference_markers.fasta -out GCF_031598375.1_ASM3159837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:09,828] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:09,832] [INFO] Selected 29 target genomes.
[2024-01-24 14:20:09,832] [INFO] Target genome list was writen to GCF_031598375.1_ASM3159837v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:09,844] [INFO] Task started: fastANI
[2024-01-24 14:20:09,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg31223f46-7f7a-43e9-8ec1-71533ce24e07/GCF_031598375.1_ASM3159837v1_genomic.fna.gz --refList GCF_031598375.1_ASM3159837v1_genomic.fna/target_genomes.txt --output GCF_031598375.1_ASM3159837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:25,606] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:25,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:25,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:25,610] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:25,610] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 14:20:25,610] [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
--------------------------------------------------------------------------------
[2024-01-24 14:20:25,612] [INFO] DFAST Taxonomy check result was written to GCF_031598375.1_ASM3159837v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:25,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:25,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:25,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/checkm_data
[2024-01-24 14:20:25,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:25,653] [INFO] Task started: CheckM
[2024-01-24 14:20:25,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031598375.1_ASM3159837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031598375.1_ASM3159837v1_genomic.fna/checkm_input GCF_031598375.1_ASM3159837v1_genomic.fna/checkm_result
[2024-01-24 14:20:55,471] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:55,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:55,497] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:55,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:55,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031598375.1_ASM3159837v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:55,498] [INFO] Task started: Blastn
[2024-01-24 14:20:55,499] [INFO] Running command: blastn -query GCF_031598375.1_ASM3159837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3cd852-90ff-4ba8-acd9-c5d25eb2be66/dqc_reference/reference_markers_gtdb.fasta -out GCF_031598375.1_ASM3159837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:56,514] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:56,518] [INFO] Selected 33 target genomes.
[2024-01-24 14:20:56,518] [INFO] Target genome list was writen to GCF_031598375.1_ASM3159837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:56,625] [INFO] Task started: fastANI
[2024-01-24 14:20:56,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg31223f46-7f7a-43e9-8ec1-71533ce24e07/GCF_031598375.1_ASM3159837v1_genomic.fna.gz --refList GCF_031598375.1_ASM3159837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031598375.1_ASM3159837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:10,445] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:10,447] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:10,447] [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
--------------------------------------------------------------------------------
[2024-01-24 14:21:10,450] [INFO] GTDB search result was written to GCF_031598375.1_ASM3159837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:10,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:10,452] [INFO] DFAST_QC result json was written to GCF_031598375.1_ASM3159837v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:10,452] [INFO] DFAST_QC completed!
[2024-01-24 14:21:10,452] [INFO] Total running time: 0h1m11s