[2023-03-14 10:55:58,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference
[2023-03-14 10:56:00,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stg54474264-8db5-4e9f-b9cf-a6c88f63ade8/OceanDNA-b21435.fa | prodigal -d OceanDNA-b21435/cds.fna -a OceanDNA-b21435/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:07,350] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:07,350] [INFO] Task started: HMMsearch
[2023-03-14 10:56:07,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b21435/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/reference_markers.hmm OceanDNA-b21435/protein.faa > /dev/null
[2023-03-14 10:56:07,536] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:07,536] [INFO] Found 6/6 markers.
[2023-03-14 10:56:07,542] [INFO] Query marker FASTA was written to OceanDNA-b21435/markers.fasta
[2023-03-14 10:56:07,542] [INFO] Task started: Blastn
[2023-03-14 10:56:07,543] [INFO] Running command: blastn -query OceanDNA-b21435/markers.fasta -db /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/reference_markers.fasta -out OceanDNA-b21435/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:08,056] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:08,057] [INFO] Selected 11 target genomes.
[2023-03-14 10:56:08,057] [INFO] Target genome list was writen to OceanDNA-b21435/target_genomes.txt
[2023-03-14 10:56:08,062] [INFO] Task started: fastANI
[2023-03-14 10:56:08,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg54474264-8db5-4e9f-b9cf-a6c88f63ade8/OceanDNA-b21435.fa --refList OceanDNA-b21435/target_genomes.txt --output OceanDNA-b21435/fastani_result.tsv --threads 1
[2023-03-14 10:56:12,776] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:12,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:12,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:12,777] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:12,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:12,777] [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 10:56:12,778] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21435/tc_result.tsv
[2023-03-14 10:56:12,778] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:12,778] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:12,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/checkm_data
[2023-03-14 10:56:12,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:12,886] [INFO] Task started: CheckM
[2023-03-14 10:56:12,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21435/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21435/checkm_input OceanDNA-b21435/checkm_result
[2023-03-14 10:56:35,477] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:35,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:35,479] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:35,480] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:35,480] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21435/markers.fasta)
[2023-03-14 10:56:35,480] [INFO] Task started: Blastn
[2023-03-14 10:56:35,480] [INFO] Running command: blastn -query OceanDNA-b21435/markers.fasta -db /var/lib/cwl/stgd4f27db3-78a2-4739-8b0e-b299db21066b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21435/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:36,224] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:36,225] [INFO] Selected 18 target genomes.
[2023-03-14 10:56:36,225] [INFO] Target genome list was writen to OceanDNA-b21435/target_genomes_gtdb.txt
[2023-03-14 10:56:36,249] [INFO] Task started: fastANI
[2023-03-14 10:56:36,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg54474264-8db5-4e9f-b9cf-a6c88f63ade8/OceanDNA-b21435.fa --refList OceanDNA-b21435/target_genomes_gtdb.txt --output OceanDNA-b21435/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:39,824] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:39,827] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:56:39,827] [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_018652595.1	s__JABIBU01 sp018652595	99.7734	286	306	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__JABIBU01	95.0	99.90	99.82	0.95	0.93	4	conclusive
--------------------------------------------------------------------------------
[2023-03-14 10:56:39,827] [INFO] GTDB search result was written to OceanDNA-b21435/result_gtdb.tsv
[2023-03-14 10:56:39,827] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:39,827] [INFO] DFAST_QC result json was written to OceanDNA-b21435/dqc_result.json
[2023-03-14 10:56:39,828] [INFO] DFAST_QC completed!
[2023-03-14 10:56:39,828] [INFO] Total running time: 0h0m41s