[2023-06-28 15:41:35,939] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:41:35,941] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:41:35,941] [INFO] DQC Reference Directory: /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference
[2023-06-28 15:41:37,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:41:37,094] [INFO] Task started: Prodigal
[2023-06-28 15:41:37,095] [INFO] Running command: gunzip -c /var/lib/cwl/stga922e23c-b4b9-4a53-a3a2-021f31ad4e24/GCA_020025075.1_ASM2002507v1_genomic.fna.gz | prodigal -d GCA_020025075.1_ASM2002507v1_genomic.fna/cds.fna -a GCA_020025075.1_ASM2002507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:41:40,602] [INFO] Task succeeded: Prodigal
[2023-06-28 15:41:40,602] [INFO] Task started: HMMsearch
[2023-06-28 15:41:40,602] [INFO] Running command: hmmsearch --tblout GCA_020025075.1_ASM2002507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/reference_markers.hmm GCA_020025075.1_ASM2002507v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:41:40,779] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:41:40,780] [INFO] Found 6/6 markers.
[2023-06-28 15:41:40,797] [INFO] Query marker FASTA was written to GCA_020025075.1_ASM2002507v1_genomic.fna/markers.fasta
[2023-06-28 15:41:40,797] [INFO] Task started: Blastn
[2023-06-28 15:41:40,797] [INFO] Running command: blastn -query GCA_020025075.1_ASM2002507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/reference_markers.fasta -out GCA_020025075.1_ASM2002507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:41:41,331] [INFO] Task succeeded: Blastn
[2023-06-28 15:41:41,334] [INFO] Selected 20 target genomes.
[2023-06-28 15:41:41,334] [INFO] Target genome list was writen to GCA_020025075.1_ASM2002507v1_genomic.fna/target_genomes.txt
[2023-06-28 15:41:41,337] [INFO] Task started: fastANI
[2023-06-28 15:41:41,337] [INFO] Running command: fastANI --query /var/lib/cwl/stga922e23c-b4b9-4a53-a3a2-021f31ad4e24/GCA_020025075.1_ASM2002507v1_genomic.fna.gz --refList GCA_020025075.1_ASM2002507v1_genomic.fna/target_genomes.txt --output GCA_020025075.1_ASM2002507v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:41:52,121] [INFO] Task succeeded: fastANI
[2023-06-28 15:41:52,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:41:52,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:41:52,123] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:41:52,123] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 15:41:52,123] [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 15:41:52,125] [INFO] DFAST Taxonomy check result was written to GCA_020025075.1_ASM2002507v1_genomic.fna/tc_result.tsv
[2023-06-28 15:41:52,125] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:41:52,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:41:52,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/checkm_data
[2023-06-28 15:41:52,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:41:52,149] [INFO] Task started: CheckM
[2023-06-28 15:41:52,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025075.1_ASM2002507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025075.1_ASM2002507v1_genomic.fna/checkm_input GCA_020025075.1_ASM2002507v1_genomic.fna/checkm_result
[2023-06-28 15:42:08,434] [INFO] Task succeeded: CheckM
[2023-06-28 15:42:08,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:42:08,451] [INFO] ===== Completeness check finished =====
[2023-06-28 15:42:08,451] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:42:08,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025075.1_ASM2002507v1_genomic.fna/markers.fasta)
[2023-06-28 15:42:08,452] [INFO] Task started: Blastn
[2023-06-28 15:42:08,452] [INFO] Running command: blastn -query GCA_020025075.1_ASM2002507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2abf977-a7f2-4e6b-84fe-dbd128e7e576/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025075.1_ASM2002507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:42:09,224] [INFO] Task succeeded: Blastn
[2023-06-28 15:42:09,227] [INFO] Selected 30 target genomes.
[2023-06-28 15:42:09,227] [INFO] Target genome list was writen to GCA_020025075.1_ASM2002507v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:42:09,240] [INFO] Task started: fastANI
[2023-06-28 15:42:09,240] [INFO] Running command: fastANI --query /var/lib/cwl/stga922e23c-b4b9-4a53-a3a2-021f31ad4e24/GCA_020025075.1_ASM2002507v1_genomic.fna.gz --refList GCA_020025075.1_ASM2002507v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025075.1_ASM2002507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:42:22,513] [INFO] Task succeeded: fastANI
[2023-06-28 15:42:22,519] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:42:22,519] [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
--------------------------------------------------------------------------------
[2023-06-28 15:42:22,521] [INFO] GTDB search result was written to GCA_020025075.1_ASM2002507v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:42:22,521] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:42:22,523] [INFO] DFAST_QC result json was written to GCA_020025075.1_ASM2002507v1_genomic.fna/dqc_result.json
[2023-06-28 15:42:22,523] [INFO] DFAST_QC completed!
[2023-06-28 15:42:22,523] [INFO] Total running time: 0h0m47s