[2023-03-17 02:31:12,850] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,850] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,378] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,378] [INFO] Running command: cat /var/lib/cwl/stg5a2f2336-bd46-4f63-945d-0a916dd037ed/OceanDNA-b5417.fa | prodigal -d OceanDNA-b5417/cds.fna -a OceanDNA-b5417/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:20,642] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:20,643] [INFO] Task started: HMMsearch
[2023-03-17 02:31:20,643] [INFO] Running command: hmmsearch --tblout OceanDNA-b5417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/reference_markers.hmm OceanDNA-b5417/protein.faa > /dev/null
[2023-03-17 02:31:20,793] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:20,793] [INFO] Found 6/6 markers.
[2023-03-17 02:31:20,806] [INFO] Query marker FASTA was written to OceanDNA-b5417/markers.fasta
[2023-03-17 02:31:20,807] [INFO] Task started: Blastn
[2023-03-17 02:31:20,807] [INFO] Running command: blastn -query OceanDNA-b5417/markers.fasta -db /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/reference_markers.fasta -out OceanDNA-b5417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:21,307] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:21,308] [INFO] Selected 28 target genomes.
[2023-03-17 02:31:21,308] [INFO] Target genome list was writen to OceanDNA-b5417/target_genomes.txt
[2023-03-17 02:31:21,325] [INFO] Task started: fastANI
[2023-03-17 02:31:21,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2f2336-bd46-4f63-945d-0a916dd037ed/OceanDNA-b5417.fa --refList OceanDNA-b5417/target_genomes.txt --output OceanDNA-b5417/fastani_result.tsv --threads 1
[2023-03-17 02:31:36,210] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:36,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:36,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:36,211] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:36,211] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:36,211] [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 02:31:36,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5417/tc_result.tsv
[2023-03-17 02:31:36,211] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:36,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:36,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/checkm_data
[2023-03-17 02:31:36,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:36,217] [INFO] Task started: CheckM
[2023-03-17 02:31:36,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5417/checkm_input OceanDNA-b5417/checkm_result
[2023-03-17 02:31:58,432] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:58,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.58%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 02:31:58,434] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:58,434] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:58,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5417/markers.fasta)
[2023-03-17 02:31:58,435] [INFO] Task started: Blastn
[2023-03-17 02:31:58,435] [INFO] Running command: blastn -query OceanDNA-b5417/markers.fasta -db /var/lib/cwl/stg03566809-159e-413e-a40a-837159ad8ba8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:59,134] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:59,136] [INFO] Selected 29 target genomes.
[2023-03-17 02:31:59,136] [INFO] Target genome list was writen to OceanDNA-b5417/target_genomes_gtdb.txt
[2023-03-17 02:32:00,138] [INFO] Task started: fastANI
[2023-03-17 02:32:00,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2f2336-bd46-4f63-945d-0a916dd037ed/OceanDNA-b5417.fa --refList OceanDNA-b5417/target_genomes_gtdb.txt --output OceanDNA-b5417/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:11,239] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:11,241] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:32:11,241] [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_002696025.1	s__UBA952 sp002696025	85.6312	83	151	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:11,241] [INFO] GTDB search result was written to OceanDNA-b5417/result_gtdb.tsv
[2023-03-17 02:32:11,241] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:11,242] [INFO] DFAST_QC result json was written to OceanDNA-b5417/dqc_result.json
[2023-03-17 02:32:11,242] [INFO] DFAST_QC completed!
[2023-03-17 02:32:11,242] [INFO] Total running time: 0h0m58s