[2023-03-19 02:59:38,330] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,330] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,330] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference
[2023-03-19 02:59:39,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,416] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,416] [INFO] Running command: cat /var/lib/cwl/stgff022149-e486-4813-86f7-998dd899560b/OceanDNA-b20511.fa | prodigal -d OceanDNA-b20511/cds.fna -a OceanDNA-b20511/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:43,639] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:43,640] [INFO] Task started: HMMsearch
[2023-03-19 02:59:43,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b20511/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/reference_markers.hmm OceanDNA-b20511/protein.faa > /dev/null
[2023-03-19 02:59:43,790] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:43,790] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgff022149-e486-4813-86f7-998dd899560b/OceanDNA-b20511.fa]
[2023-03-19 02:59:43,802] [INFO] Query marker FASTA was written to OceanDNA-b20511/markers.fasta
[2023-03-19 02:59:43,804] [INFO] Task started: Blastn
[2023-03-19 02:59:43,804] [INFO] Running command: blastn -query OceanDNA-b20511/markers.fasta -db /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/reference_markers.fasta -out OceanDNA-b20511/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:44,345] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:44,345] [INFO] Selected 15 target genomes.
[2023-03-19 02:59:44,346] [INFO] Target genome list was writen to OceanDNA-b20511/target_genomes.txt
[2023-03-19 02:59:44,353] [INFO] Task started: fastANI
[2023-03-19 02:59:44,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgff022149-e486-4813-86f7-998dd899560b/OceanDNA-b20511.fa --refList OceanDNA-b20511/target_genomes.txt --output OceanDNA-b20511/fastani_result.tsv --threads 1
[2023-03-19 02:59:51,009] [INFO] Task succeeded: fastANI
[2023-03-19 02:59:51,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:59:51,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:59:51,009] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:59:51,010] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:59:51,010] [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
--------------------------------------------------------------------------------
[2023-03-19 02:59:51,010] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20511/tc_result.tsv
[2023-03-19 02:59:51,010] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:59:51,010] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:59:51,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/checkm_data
[2023-03-19 02:59:51,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:59:51,173] [INFO] Task started: CheckM
[2023-03-19 02:59:51,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20511/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20511/checkm_input OceanDNA-b20511/checkm_result
[2023-03-19 03:00:07,759] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:07,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:07,761] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:07,761] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:07,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20511/markers.fasta)
[2023-03-19 03:00:07,761] [INFO] Task started: Blastn
[2023-03-19 03:00:07,761] [INFO] Running command: blastn -query OceanDNA-b20511/markers.fasta -db /var/lib/cwl/stgd1ddf595-5c13-4329-a0ef-693e28d9a49c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20511/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:08,456] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:08,457] [INFO] Selected 20 target genomes.
[2023-03-19 03:00:08,457] [INFO] Target genome list was writen to OceanDNA-b20511/target_genomes_gtdb.txt
[2023-03-19 03:00:08,482] [INFO] Task started: fastANI
[2023-03-19 03:00:08,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgff022149-e486-4813-86f7-998dd899560b/OceanDNA-b20511.fa --refList OceanDNA-b20511/target_genomes_gtdb.txt --output OceanDNA-b20511/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:14,828] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:14,828] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:00:14,828] [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
--------------------------------------------------------------------------------
[2023-03-19 03:00:14,828] [INFO] GTDB search result was written to OceanDNA-b20511/result_gtdb.tsv
[2023-03-19 03:00:14,828] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:14,829] [INFO] DFAST_QC result json was written to OceanDNA-b20511/dqc_result.json
[2023-03-19 03:00:14,829] [INFO] DFAST_QC completed!
[2023-03-19 03:00:14,829] [INFO] Total running time: 0h0m36s