[2023-03-18 08:17:18,477] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,478] [INFO] DQC Reference Directory: /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference
[2023-03-18 08:17:20,262] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,262] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,262] [INFO] Running command: cat /var/lib/cwl/stgdf645e3e-5e5c-426a-961c-b0f8266158e4/OceanDNA-b20646.fa | prodigal -d OceanDNA-b20646/cds.fna -a OceanDNA-b20646/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:25,901] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:25,901] [INFO] Task started: HMMsearch
[2023-03-18 08:17:25,901] [INFO] Running command: hmmsearch --tblout OceanDNA-b20646/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/reference_markers.hmm OceanDNA-b20646/protein.faa > /dev/null
[2023-03-18 08:17:26,040] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:26,040] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdf645e3e-5e5c-426a-961c-b0f8266158e4/OceanDNA-b20646.fa]
[2023-03-18 08:17:26,052] [INFO] Query marker FASTA was written to OceanDNA-b20646/markers.fasta
[2023-03-18 08:17:26,052] [INFO] Task started: Blastn
[2023-03-18 08:17:26,052] [INFO] Running command: blastn -query OceanDNA-b20646/markers.fasta -db /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/reference_markers.fasta -out OceanDNA-b20646/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:26,562] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:26,562] [INFO] Selected 21 target genomes.
[2023-03-18 08:17:26,563] [INFO] Target genome list was writen to OceanDNA-b20646/target_genomes.txt
[2023-03-18 08:17:26,574] [INFO] Task started: fastANI
[2023-03-18 08:17:26,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf645e3e-5e5c-426a-961c-b0f8266158e4/OceanDNA-b20646.fa --refList OceanDNA-b20646/target_genomes.txt --output OceanDNA-b20646/fastani_result.tsv --threads 1
[2023-03-18 08:17:38,212] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:38,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:38,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:38,213] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:38,213] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:38,213] [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
--------------------------------------------------------------------------------
[2023-03-18 08:17:38,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20646/tc_result.tsv
[2023-03-18 08:17:38,213] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:38,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:38,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/checkm_data
[2023-03-18 08:17:38,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:38,219] [INFO] Task started: CheckM
[2023-03-18 08:17:38,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20646/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20646/checkm_input OceanDNA-b20646/checkm_result
[2023-03-18 08:17:58,382] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:58,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 3.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 08:17:58,385] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:58,385] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:58,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20646/markers.fasta)
[2023-03-18 08:17:58,385] [INFO] Task started: Blastn
[2023-03-18 08:17:58,385] [INFO] Running command: blastn -query OceanDNA-b20646/markers.fasta -db /var/lib/cwl/stga6c5fd92-903d-4187-a70a-abfca0669c51/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20646/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:59,025] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:59,026] [INFO] Selected 22 target genomes.
[2023-03-18 08:17:59,026] [INFO] Target genome list was writen to OceanDNA-b20646/target_genomes_gtdb.txt
[2023-03-18 08:17:59,108] [INFO] Task started: fastANI
[2023-03-18 08:17:59,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf645e3e-5e5c-426a-961c-b0f8266158e4/OceanDNA-b20646.fa --refList OceanDNA-b20646/target_genomes_gtdb.txt --output OceanDNA-b20646/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:09,987] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:09,989] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:09,989] [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_018671635.1	s__JABHHG01 sp018671635	82.2581	231	347	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__JABHHG01	95.0	99.09	99.01	0.82	0.76	4	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:09,989] [INFO] GTDB search result was written to OceanDNA-b20646/result_gtdb.tsv
[2023-03-18 08:18:09,989] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:09,989] [INFO] DFAST_QC result json was written to OceanDNA-b20646/dqc_result.json
[2023-03-18 08:18:09,989] [INFO] DFAST_QC completed!
[2023-03-18 08:18:09,989] [INFO] Total running time: 0h0m52s