[2023-03-18 03:45:10,238] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,238] [INFO] DQC Reference Directory: /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference
[2023-03-18 03:45:11,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,968] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,968] [INFO] Running command: cat /var/lib/cwl/stg9749497f-1d90-4e8c-90ba-58cced91cc76/OceanDNA-b23229.fa | prodigal -d OceanDNA-b23229/cds.fna -a OceanDNA-b23229/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:43,003] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:43,003] [INFO] Task started: HMMsearch
[2023-03-18 03:45:43,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b23229/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/reference_markers.hmm OceanDNA-b23229/protein.faa > /dev/null
[2023-03-18 03:45:43,232] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:43,232] [INFO] Found 6/6 markers.
[2023-03-18 03:45:43,266] [INFO] Query marker FASTA was written to OceanDNA-b23229/markers.fasta
[2023-03-18 03:45:43,266] [INFO] Task started: Blastn
[2023-03-18 03:45:43,266] [INFO] Running command: blastn -query OceanDNA-b23229/markers.fasta -db /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/reference_markers.fasta -out OceanDNA-b23229/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:43,765] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:43,766] [INFO] Selected 5 target genomes.
[2023-03-18 03:45:43,766] [INFO] Target genome list was writen to OceanDNA-b23229/target_genomes.txt
[2023-03-18 03:45:43,769] [INFO] Task started: fastANI
[2023-03-18 03:45:43,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg9749497f-1d90-4e8c-90ba-58cced91cc76/OceanDNA-b23229.fa --refList OceanDNA-b23229/target_genomes.txt --output OceanDNA-b23229/fastani_result.tsv --threads 1
[2023-03-18 03:45:46,747] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:46,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:46,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:46,748] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:46,748] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:46,748] [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 03:45:46,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23229/tc_result.tsv
[2023-03-18 03:45:46,748] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:46,748] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:46,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/checkm_data
[2023-03-18 03:45:46,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:46,757] [INFO] Task started: CheckM
[2023-03-18 03:45:46,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23229/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23229/checkm_input OceanDNA-b23229/checkm_result
[2023-03-18 03:47:02,602] [INFO] Task succeeded: CheckM
[2023-03-18 03:47:02,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:47:02,606] [INFO] ===== Completeness check finished =====
[2023-03-18 03:47:02,606] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:47:02,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23229/markers.fasta)
[2023-03-18 03:47:02,606] [INFO] Task started: Blastn
[2023-03-18 03:47:02,606] [INFO] Running command: blastn -query OceanDNA-b23229/markers.fasta -db /var/lib/cwl/stgfed15187-77d7-4b61-a76c-3fe86580835a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23229/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:47:03,274] [INFO] Task succeeded: Blastn
[2023-03-18 03:47:03,275] [INFO] Selected 6 target genomes.
[2023-03-18 03:47:03,275] [INFO] Target genome list was writen to OceanDNA-b23229/target_genomes_gtdb.txt
[2023-03-18 03:47:03,305] [INFO] Task started: fastANI
[2023-03-18 03:47:03,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg9749497f-1d90-4e8c-90ba-58cced91cc76/OceanDNA-b23229.fa --refList OceanDNA-b23229/target_genomes_gtdb.txt --output OceanDNA-b23229/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:08,380] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:08,383] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:47:08,383] [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_002697225.1	s__UBA9662 sp002697225	98.0082	1163	1862	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	97.07	96.17	0.75	0.62	4	conclusive
GCA_012963885.1	s__UBA9662 sp012963885	85.2258	1493	1862	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	99.64	99.54	0.93	0.91	4	-
GCA_002709695.1	s__UBA9662 sp002709695	84.7076	1360	1862	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__UBA9662;g__UBA9662	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:08,548] [INFO] GTDB search result was written to OceanDNA-b23229/result_gtdb.tsv
[2023-03-18 03:47:08,563] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:08,564] [INFO] DFAST_QC result json was written to OceanDNA-b23229/dqc_result.json
[2023-03-18 03:47:08,564] [INFO] DFAST_QC completed!
[2023-03-18 03:47:08,564] [INFO] Total running time: 0h1m58s