[2023-03-17 07:28:30,366] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,366] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,366] [INFO] DQC Reference Directory: /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stg4a3021b8-f03d-4790-b380-74ccb4fd6f3a/OceanDNA-b28588.fa | prodigal -d OceanDNA-b28588/cds.fna -a OceanDNA-b28588/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:43,081] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:43,082] [INFO] Task started: HMMsearch
[2023-03-17 07:28:43,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b28588/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/reference_markers.hmm OceanDNA-b28588/protein.faa > /dev/null
[2023-03-17 07:28:43,266] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:43,267] [INFO] Found 6/6 markers.
[2023-03-17 07:28:43,284] [INFO] Query marker FASTA was written to OceanDNA-b28588/markers.fasta
[2023-03-17 07:28:43,284] [INFO] Task started: Blastn
[2023-03-17 07:28:43,284] [INFO] Running command: blastn -query OceanDNA-b28588/markers.fasta -db /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/reference_markers.fasta -out OceanDNA-b28588/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:43,804] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:43,805] [INFO] Selected 27 target genomes.
[2023-03-17 07:28:43,805] [INFO] Target genome list was writen to OceanDNA-b28588/target_genomes.txt
[2023-03-17 07:28:43,817] [INFO] Task started: fastANI
[2023-03-17 07:28:43,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a3021b8-f03d-4790-b380-74ccb4fd6f3a/OceanDNA-b28588.fa --refList OceanDNA-b28588/target_genomes.txt --output OceanDNA-b28588/fastani_result.tsv --threads 1
[2023-03-17 07:28:58,863] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:58,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:58,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:58,864] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:58,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:58,864] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:58,864] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28588/tc_result.tsv
[2023-03-17 07:28:58,865] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:58,865] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:58,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/checkm_data
[2023-03-17 07:28:58,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:58,872] [INFO] Task started: CheckM
[2023-03-17 07:28:58,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28588/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28588/checkm_input OceanDNA-b28588/checkm_result
[2023-03-17 07:29:31,996] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:31,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.01%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:31,998] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:31,999] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:31,999] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28588/markers.fasta)
[2023-03-17 07:29:31,999] [INFO] Task started: Blastn
[2023-03-17 07:29:31,999] [INFO] Running command: blastn -query OceanDNA-b28588/markers.fasta -db /var/lib/cwl/stga1e5448c-818e-461f-b1d1-a922d7b26759/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28588/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:32,697] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:32,698] [INFO] Selected 29 target genomes.
[2023-03-17 07:29:32,698] [INFO] Target genome list was writen to OceanDNA-b28588/target_genomes_gtdb.txt
[2023-03-17 07:29:32,995] [INFO] Task started: fastANI
[2023-03-17 07:29:32,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a3021b8-f03d-4790-b380-74ccb4fd6f3a/OceanDNA-b28588.fa --refList OceanDNA-b28588/target_genomes_gtdb.txt --output OceanDNA-b28588/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:47,755] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:47,757] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:47,757] [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_001510135.1	s__LFER01 sp001510135	77.6736	233	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:47,757] [INFO] GTDB search result was written to OceanDNA-b28588/result_gtdb.tsv
[2023-03-17 07:29:47,757] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:47,758] [INFO] DFAST_QC result json was written to OceanDNA-b28588/dqc_result.json
[2023-03-17 07:29:47,758] [INFO] DFAST_QC completed!
[2023-03-17 07:29:47,758] [INFO] Total running time: 0h1m17s