[2023-03-14 13:55:26,682] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:55:26,682] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:55:26,682] [INFO] DQC Reference Directory: /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference
[2023-03-14 13:55:29,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:55:29,062] [INFO] Task started: Prodigal
[2023-03-14 13:55:29,062] [INFO] Running command: cat /var/lib/cwl/stg9a45be40-1f95-4c56-b5e7-5720afd7a45b/OceanDNA-b21690.fa | prodigal -d OceanDNA-b21690/cds.fna -a OceanDNA-b21690/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:55:37,878] [INFO] Task succeeded: Prodigal
[2023-03-14 13:55:37,878] [INFO] Task started: HMMsearch
[2023-03-14 13:55:37,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b21690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/reference_markers.hmm OceanDNA-b21690/protein.faa > /dev/null
[2023-03-14 13:55:38,199] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:55:38,200] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9a45be40-1f95-4c56-b5e7-5720afd7a45b/OceanDNA-b21690.fa]
[2023-03-14 13:55:38,208] [INFO] Query marker FASTA was written to OceanDNA-b21690/markers.fasta
[2023-03-14 13:55:38,209] [INFO] Task started: Blastn
[2023-03-14 13:55:38,209] [INFO] Running command: blastn -query OceanDNA-b21690/markers.fasta -db /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/reference_markers.fasta -out OceanDNA-b21690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:55:38,818] [INFO] Task succeeded: Blastn
[2023-03-14 13:55:38,819] [INFO] Selected 14 target genomes.
[2023-03-14 13:55:38,819] [INFO] Target genome list was writen to OceanDNA-b21690/target_genomes.txt
[2023-03-14 13:55:38,826] [INFO] Task started: fastANI
[2023-03-14 13:55:38,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a45be40-1f95-4c56-b5e7-5720afd7a45b/OceanDNA-b21690.fa --refList OceanDNA-b21690/target_genomes.txt --output OceanDNA-b21690/fastani_result.tsv --threads 1
[2023-03-14 13:55:47,044] [INFO] Task succeeded: fastANI
[2023-03-14 13:55:47,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:55:47,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:55:47,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:55:47,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:55:47,045] [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
--------------------------------------------------------------------------------
[2023-03-14 13:55:47,045] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21690/tc_result.tsv
[2023-03-14 13:55:47,046] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:55:47,046] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:55:47,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/checkm_data
[2023-03-14 13:55:47,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:55:47,051] [INFO] Task started: CheckM
[2023-03-14 13:55:47,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21690/checkm_input OceanDNA-b21690/checkm_result
[2023-03-14 13:56:08,814] [INFO] Task succeeded: CheckM
[2023-03-14 13:56:08,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:56:08,816] [INFO] ===== Completeness check finished =====
[2023-03-14 13:56:08,816] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:56:08,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21690/markers.fasta)
[2023-03-14 13:56:08,817] [INFO] Task started: Blastn
[2023-03-14 13:56:08,817] [INFO] Running command: blastn -query OceanDNA-b21690/markers.fasta -db /var/lib/cwl/stgb716b2fc-f402-45bb-b804-9533fb2af5e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:56:10,654] [INFO] Task succeeded: Blastn
[2023-03-14 13:56:10,655] [INFO] Selected 22 target genomes.
[2023-03-14 13:56:10,655] [INFO] Target genome list was writen to OceanDNA-b21690/target_genomes_gtdb.txt
[2023-03-14 13:56:10,674] [INFO] Task started: fastANI
[2023-03-14 13:56:10,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a45be40-1f95-4c56-b5e7-5720afd7a45b/OceanDNA-b21690.fa --refList OceanDNA-b21690/target_genomes_gtdb.txt --output OceanDNA-b21690/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:56:25,783] [INFO] Task succeeded: fastANI
[2023-03-14 13:56:25,783] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:56:25,783] [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
--------------------------------------------------------------------------------
[2023-03-14 13:56:25,783] [INFO] GTDB search result was written to OceanDNA-b21690/result_gtdb.tsv
[2023-03-14 13:56:25,783] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:56:25,784] [INFO] DFAST_QC result json was written to OceanDNA-b21690/dqc_result.json
[2023-03-14 13:56:25,784] [INFO] DFAST_QC completed!
[2023-03-14 13:56:25,784] [INFO] Total running time: 0h0m59s