[2023-03-15 08:59:48,894] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:48,894] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:48,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference
[2023-03-15 08:59:50,065] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:50,065] [INFO] Task started: Prodigal
[2023-03-15 08:59:50,065] [INFO] Running command: cat /var/lib/cwl/stgd483640b-0b56-435e-b190-a388d0a04296/OceanDNA-b40175.fa | prodigal -d OceanDNA-b40175/cds.fna -a OceanDNA-b40175/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:00,480] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:00,480] [INFO] Task started: HMMsearch
[2023-03-15 09:00:00,480] [INFO] Running command: hmmsearch --tblout OceanDNA-b40175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/reference_markers.hmm OceanDNA-b40175/protein.faa > /dev/null
[2023-03-15 09:00:00,686] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:00,687] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd483640b-0b56-435e-b190-a388d0a04296/OceanDNA-b40175.fa]
[2023-03-15 09:00:00,704] [INFO] Query marker FASTA was written to OceanDNA-b40175/markers.fasta
[2023-03-15 09:00:00,704] [INFO] Task started: Blastn
[2023-03-15 09:00:00,704] [INFO] Running command: blastn -query OceanDNA-b40175/markers.fasta -db /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/reference_markers.fasta -out OceanDNA-b40175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:01,292] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:01,293] [INFO] Selected 27 target genomes.
[2023-03-15 09:00:01,293] [INFO] Target genome list was writen to OceanDNA-b40175/target_genomes.txt
[2023-03-15 09:00:01,307] [INFO] Task started: fastANI
[2023-03-15 09:00:01,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgd483640b-0b56-435e-b190-a388d0a04296/OceanDNA-b40175.fa --refList OceanDNA-b40175/target_genomes.txt --output OceanDNA-b40175/fastani_result.tsv --threads 1
[2023-03-15 09:00:16,160] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:16,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:16,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:16,161] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:16,161] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:00:16,161] [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 09:00:16,161] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40175/tc_result.tsv
[2023-03-15 09:00:16,161] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:16,162] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:16,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/checkm_data
[2023-03-15 09:00:16,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:16,168] [INFO] Task started: CheckM
[2023-03-15 09:00:16,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40175/checkm_input OceanDNA-b40175/checkm_result
[2023-03-15 09:00:46,406] [INFO] Task succeeded: CheckM
[2023-03-15 09:00:46,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:00:46,409] [INFO] ===== Completeness check finished =====
[2023-03-15 09:00:46,409] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:00:46,409] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40175/markers.fasta)
[2023-03-15 09:00:46,409] [INFO] Task started: Blastn
[2023-03-15 09:00:46,409] [INFO] Running command: blastn -query OceanDNA-b40175/markers.fasta -db /var/lib/cwl/stg9c59d759-e0ca-4994-befc-fb681c4c0d24/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:47,334] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:47,335] [INFO] Selected 19 target genomes.
[2023-03-15 09:00:47,335] [INFO] Target genome list was writen to OceanDNA-b40175/target_genomes_gtdb.txt
[2023-03-15 09:00:47,360] [INFO] Task started: fastANI
[2023-03-15 09:00:47,361] [INFO] Running command: fastANI --query /var/lib/cwl/stgd483640b-0b56-435e-b190-a388d0a04296/OceanDNA-b40175.fa --refList OceanDNA-b40175/target_genomes_gtdb.txt --output OceanDNA-b40175/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:00:56,929] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:56,932] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:00:56,932] [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_905181995.1	s__TMED48 sp905181995	98.7	412	536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002339165.1	s__TMED48 sp002339165	91.9684	462	536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:00:56,932] [INFO] GTDB search result was written to OceanDNA-b40175/result_gtdb.tsv
[2023-03-15 09:00:56,932] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:00:56,933] [INFO] DFAST_QC result json was written to OceanDNA-b40175/dqc_result.json
[2023-03-15 09:00:56,933] [INFO] DFAST_QC completed!
[2023-03-15 09:00:56,933] [INFO] Total running time: 0h1m8s