[2023-03-16 03:23:49,857] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,858] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference
[2023-03-16 03:23:51,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:51,045] [INFO] Task started: Prodigal
[2023-03-16 03:23:51,045] [INFO] Running command: cat /var/lib/cwl/stgf8accf35-1474-4b02-b8ec-eb091d7c55eb/OceanDNA-b16778.fa | prodigal -d OceanDNA-b16778/cds.fna -a OceanDNA-b16778/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:05,503] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:05,504] [INFO] Task started: HMMsearch
[2023-03-16 03:24:05,504] [INFO] Running command: hmmsearch --tblout OceanDNA-b16778/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/reference_markers.hmm OceanDNA-b16778/protein.faa > /dev/null
[2023-03-16 03:24:05,749] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:05,749] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8accf35-1474-4b02-b8ec-eb091d7c55eb/OceanDNA-b16778.fa]
[2023-03-16 03:24:05,779] [INFO] Query marker FASTA was written to OceanDNA-b16778/markers.fasta
[2023-03-16 03:24:05,779] [INFO] Task started: Blastn
[2023-03-16 03:24:05,779] [INFO] Running command: blastn -query OceanDNA-b16778/markers.fasta -db /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/reference_markers.fasta -out OceanDNA-b16778/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:06,261] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:06,262] [INFO] Selected 11 target genomes.
[2023-03-16 03:24:06,262] [INFO] Target genome list was writen to OceanDNA-b16778/target_genomes.txt
[2023-03-16 03:24:06,272] [INFO] Task started: fastANI
[2023-03-16 03:24:06,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8accf35-1474-4b02-b8ec-eb091d7c55eb/OceanDNA-b16778.fa --refList OceanDNA-b16778/target_genomes.txt --output OceanDNA-b16778/fastani_result.tsv --threads 1
[2023-03-16 03:24:13,495] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:13,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:13,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:13,496] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:13,496] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:13,496] [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
--------------------------------------------------------------------------------
[2023-03-16 03:24:13,496] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16778/tc_result.tsv
[2023-03-16 03:24:13,496] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:13,496] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:13,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/checkm_data
[2023-03-16 03:24:13,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:13,504] [INFO] Task started: CheckM
[2023-03-16 03:24:13,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16778/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16778/checkm_input OceanDNA-b16778/checkm_result
[2023-03-16 03:24:53,664] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:53,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:53,668] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:53,668] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:53,668] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16778/markers.fasta)
[2023-03-16 03:24:53,669] [INFO] Task started: Blastn
[2023-03-16 03:24:53,669] [INFO] Running command: blastn -query OceanDNA-b16778/markers.fasta -db /var/lib/cwl/stgf494ac58-1d42-421b-9ac7-046c9b3a7ad5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16778/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:54,106] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:54,107] [INFO] Selected 21 target genomes.
[2023-03-16 03:24:54,107] [INFO] Target genome list was writen to OceanDNA-b16778/target_genomes_gtdb.txt
[2023-03-16 03:24:54,841] [INFO] Task started: fastANI
[2023-03-16 03:24:54,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8accf35-1474-4b02-b8ec-eb091d7c55eb/OceanDNA-b16778.fa --refList OceanDNA-b16778/target_genomes_gtdb.txt --output OceanDNA-b16778/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:08,345] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:08,347] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:08,347] [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_016124935.1	s__RI-106 sp016124935	77.5962	99	605	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__RI-106	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:08,347] [INFO] GTDB search result was written to OceanDNA-b16778/result_gtdb.tsv
[2023-03-16 03:25:08,348] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:08,348] [INFO] DFAST_QC result json was written to OceanDNA-b16778/dqc_result.json
[2023-03-16 03:25:08,348] [INFO] DFAST_QC completed!
[2023-03-16 03:25:08,348] [INFO] Total running time: 0h1m18s