[2023-06-05 10:46:57,289] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:46:57,292] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:46:57,293] [INFO] DQC Reference Directory: /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference
[2023-06-05 10:46:58,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:46:58,766] [INFO] Task started: Prodigal
[2023-06-05 10:46:58,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg48395b35-d55d-416d-875b-ab3564c210bb/GCA_001004285.1_ASM100428v1_genomic.fna.gz | prodigal -d GCA_001004285.1_ASM100428v1_genomic.fna/cds.fna -a GCA_001004285.1_ASM100428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:47:01,632] [INFO] Task succeeded: Prodigal
[2023-06-05 10:47:01,632] [INFO] Task started: HMMsearch
[2023-06-05 10:47:01,633] [INFO] Running command: hmmsearch --tblout GCA_001004285.1_ASM100428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/reference_markers.hmm GCA_001004285.1_ASM100428v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:47:01,777] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:47:01,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48395b35-d55d-416d-875b-ab3564c210bb/GCA_001004285.1_ASM100428v1_genomic.fna.gz]
[2023-06-05 10:47:01,790] [INFO] Query marker FASTA was written to GCA_001004285.1_ASM100428v1_genomic.fna/markers.fasta
[2023-06-05 10:47:01,791] [INFO] Task started: Blastn
[2023-06-05 10:47:01,791] [INFO] Running command: blastn -query GCA_001004285.1_ASM100428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/reference_markers.fasta -out GCA_001004285.1_ASM100428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:02,347] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:02,350] [INFO] Selected 14 target genomes.
[2023-06-05 10:47:02,351] [INFO] Target genome list was writen to GCA_001004285.1_ASM100428v1_genomic.fna/target_genomes.txt
[2023-06-05 10:47:02,355] [INFO] Task started: fastANI
[2023-06-05 10:47:02,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg48395b35-d55d-416d-875b-ab3564c210bb/GCA_001004285.1_ASM100428v1_genomic.fna.gz --refList GCA_001004285.1_ASM100428v1_genomic.fna/target_genomes.txt --output GCA_001004285.1_ASM100428v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:47:12,208] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:12,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:47:12,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:47:12,210] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:47:12,210] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:47:12,210] [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
--------------------------------------------------------------------------------
[2023-06-05 10:47:12,212] [INFO] DFAST Taxonomy check result was written to GCA_001004285.1_ASM100428v1_genomic.fna/tc_result.tsv
[2023-06-05 10:47:12,212] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:47:12,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:47:12,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/checkm_data
[2023-06-05 10:47:12,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:47:12,225] [INFO] Task started: CheckM
[2023-06-05 10:47:12,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001004285.1_ASM100428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001004285.1_ASM100428v1_genomic.fna/checkm_input GCA_001004285.1_ASM100428v1_genomic.fna/checkm_result
[2023-06-05 10:47:27,361] [INFO] Task succeeded: CheckM
[2023-06-05 10:47:27,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 6.25%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-05 10:47:27,377] [INFO] ===== Completeness check finished =====
[2023-06-05 10:47:27,378] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:47:27,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001004285.1_ASM100428v1_genomic.fna/markers.fasta)
[2023-06-05 10:47:27,378] [INFO] Task started: Blastn
[2023-06-05 10:47:27,378] [INFO] Running command: blastn -query GCA_001004285.1_ASM100428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d1b30a-11d7-42de-8081-2abd5f89b8cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_001004285.1_ASM100428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:28,156] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:28,159] [INFO] Selected 14 target genomes.
[2023-06-05 10:47:28,159] [INFO] Target genome list was writen to GCA_001004285.1_ASM100428v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:47:28,207] [INFO] Task started: fastANI
[2023-06-05 10:47:28,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg48395b35-d55d-416d-875b-ab3564c210bb/GCA_001004285.1_ASM100428v1_genomic.fna.gz --refList GCA_001004285.1_ASM100428v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001004285.1_ASM100428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:47:33,661] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:33,663] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 10:47:33,663] [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
--------------------------------------------------------------------------------
[2023-06-05 10:47:33,665] [INFO] GTDB search result was written to GCA_001004285.1_ASM100428v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:47:33,665] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:47:33,667] [INFO] DFAST_QC result json was written to GCA_001004285.1_ASM100428v1_genomic.fna/dqc_result.json
[2023-06-05 10:47:33,667] [INFO] DFAST_QC completed!
[2023-06-05 10:47:33,667] [INFO] Total running time: 0h0m36s