[2023-03-15 23:58:53,717] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:58:53,719] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:58:53,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference
[2023-03-15 23:58:54,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:58:54,832] [INFO] Task started: Prodigal
[2023-03-15 23:58:54,832] [INFO] Running command: cat /var/lib/cwl/stg96f5e8ee-b9c6-4f16-b1ad-c993ed4e7a4d/OceanDNA-b25399.fa | prodigal -d OceanDNA-b25399/cds.fna -a OceanDNA-b25399/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:58:56,915] [INFO] Task succeeded: Prodigal
[2023-03-15 23:58:56,915] [INFO] Task started: HMMsearch
[2023-03-15 23:58:56,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b25399/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/reference_markers.hmm OceanDNA-b25399/protein.faa > /dev/null
[2023-03-15 23:58:57,034] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:58:57,035] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg96f5e8ee-b9c6-4f16-b1ad-c993ed4e7a4d/OceanDNA-b25399.fa]
[2023-03-15 23:58:57,053] [INFO] Query marker FASTA was written to OceanDNA-b25399/markers.fasta
[2023-03-15 23:58:57,055] [INFO] Task started: Blastn
[2023-03-15 23:58:57,055] [INFO] Running command: blastn -query OceanDNA-b25399/markers.fasta -db /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/reference_markers.fasta -out OceanDNA-b25399/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:58:57,576] [INFO] Task succeeded: Blastn
[2023-03-15 23:58:57,580] [INFO] Selected 11 target genomes.
[2023-03-15 23:58:57,580] [INFO] Target genome list was writen to OceanDNA-b25399/target_genomes.txt
[2023-03-15 23:58:57,599] [INFO] Task started: fastANI
[2023-03-15 23:58:57,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f5e8ee-b9c6-4f16-b1ad-c993ed4e7a4d/OceanDNA-b25399.fa --refList OceanDNA-b25399/target_genomes.txt --output OceanDNA-b25399/fastani_result.tsv --threads 1
[2023-03-15 23:59:01,555] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:01,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:59:01,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:59:01,555] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:59:01,555] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:59:01,555] [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
--------------------------------------------------------------------------------
[2023-03-15 23:59:01,557] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25399/tc_result.tsv
[2023-03-15 23:59:01,558] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:59:01,559] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:59:01,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/checkm_data
[2023-03-15 23:59:01,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:59:01,571] [INFO] Task started: CheckM
[2023-03-15 23:59:01,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25399/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25399/checkm_input OceanDNA-b25399/checkm_result
[2023-03-15 23:59:14,285] [INFO] Task succeeded: CheckM
[2023-03-15 23:59:14,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.80%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:59:14,336] [INFO] ===== Completeness check finished =====
[2023-03-15 23:59:14,336] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:59:14,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25399/markers.fasta)
[2023-03-15 23:59:14,338] [INFO] Task started: Blastn
[2023-03-15 23:59:14,338] [INFO] Running command: blastn -query OceanDNA-b25399/markers.fasta -db /var/lib/cwl/stgb83aac00-8d7d-448e-99c4-189dc1d2ae1b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25399/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:15,221] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:15,226] [INFO] Selected 21 target genomes.
[2023-03-15 23:59:15,226] [INFO] Target genome list was writen to OceanDNA-b25399/target_genomes_gtdb.txt
[2023-03-15 23:59:15,287] [INFO] Task started: fastANI
[2023-03-15 23:59:15,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f5e8ee-b9c6-4f16-b1ad-c993ed4e7a4d/OceanDNA-b25399.fa --refList OceanDNA-b25399/target_genomes_gtdb.txt --output OceanDNA-b25399/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:59:18,398] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:18,400] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:59:18,400] [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
GCA_902606835.1	s__AG-414-E02 sp902606835	78.7589	51	79	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:59:18,405] [INFO] GTDB search result was written to OceanDNA-b25399/result_gtdb.tsv
[2023-03-15 23:59:18,409] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:59:18,412] [INFO] DFAST_QC result json was written to OceanDNA-b25399/dqc_result.json
[2023-03-15 23:59:18,413] [INFO] DFAST_QC completed!
[2023-03-15 23:59:18,413] [INFO] Total running time: 0h0m25s