[2023-03-14 12:03:55,350] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference
[2023-03-14 12:03:56,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,868] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,868] [INFO] Running command: cat /var/lib/cwl/stgceed7ffa-1ee4-473e-9cee-84998041d130/OceanDNA-b35879.fa | prodigal -d OceanDNA-b35879/cds.fna -a OceanDNA-b35879/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:01,232] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:01,232] [INFO] Task started: HMMsearch
[2023-03-14 12:04:01,232] [INFO] Running command: hmmsearch --tblout OceanDNA-b35879/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/reference_markers.hmm OceanDNA-b35879/protein.faa > /dev/null
[2023-03-14 12:04:01,408] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:01,408] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgceed7ffa-1ee4-473e-9cee-84998041d130/OceanDNA-b35879.fa]
[2023-03-14 12:04:01,434] [INFO] Query marker FASTA was written to OceanDNA-b35879/markers.fasta
[2023-03-14 12:04:01,435] [INFO] Task started: Blastn
[2023-03-14 12:04:01,435] [INFO] Running command: blastn -query OceanDNA-b35879/markers.fasta -db /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/reference_markers.fasta -out OceanDNA-b35879/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:02,716] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:02,721] [INFO] Selected 11 target genomes.
[2023-03-14 12:04:02,721] [INFO] Target genome list was writen to OceanDNA-b35879/target_genomes.txt
[2023-03-14 12:04:02,729] [INFO] Task started: fastANI
[2023-03-14 12:04:02,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgceed7ffa-1ee4-473e-9cee-84998041d130/OceanDNA-b35879.fa --refList OceanDNA-b35879/target_genomes.txt --output OceanDNA-b35879/fastani_result.tsv --threads 1
[2023-03-14 12:04:08,789] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:08,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:08,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:08,790] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:08,790] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:04:08,790] [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 12:04:08,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35879/tc_result.tsv
[2023-03-14 12:04:08,794] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:08,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:08,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/checkm_data
[2023-03-14 12:04:08,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:09,057] [INFO] Task started: CheckM
[2023-03-14 12:04:09,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35879/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35879/checkm_input OceanDNA-b35879/checkm_result
[2023-03-14 12:04:26,570] [INFO] Task succeeded: CheckM
[2023-03-14 12:04:26,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:04:26,618] [INFO] ===== Completeness check finished =====
[2023-03-14 12:04:26,619] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:04:26,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35879/markers.fasta)
[2023-03-14 12:04:26,620] [INFO] Task started: Blastn
[2023-03-14 12:04:26,620] [INFO] Running command: blastn -query OceanDNA-b35879/markers.fasta -db /var/lib/cwl/stgcace955d-a744-4f0e-ae6b-689022dd4050/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35879/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:27,445] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:27,450] [INFO] Selected 22 target genomes.
[2023-03-14 12:04:27,450] [INFO] Target genome list was writen to OceanDNA-b35879/target_genomes_gtdb.txt
[2023-03-14 12:04:27,529] [INFO] Task started: fastANI
[2023-03-14 12:04:27,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgceed7ffa-1ee4-473e-9cee-84998041d130/OceanDNA-b35879.fa --refList OceanDNA-b35879/target_genomes_gtdb.txt --output OceanDNA-b35879/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:04:35,783] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:35,785] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:04:35,785] [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_002170535.1	s__TMED69 sp002170535	80.6279	166	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536_A;f__Ga0077536_A;g__TMED69	95.0	96.40	96.40	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:04:35,787] [INFO] GTDB search result was written to OceanDNA-b35879/result_gtdb.tsv
[2023-03-14 12:04:35,788] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:04:35,790] [INFO] DFAST_QC result json was written to OceanDNA-b35879/dqc_result.json
[2023-03-14 12:04:35,790] [INFO] DFAST_QC completed!
[2023-03-14 12:04:35,790] [INFO] Total running time: 0h0m40s