[2023-03-18 05:17:48,232] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:17:48,233] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:17:48,233] [INFO] DQC Reference Directory: /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference
[2023-03-18 05:17:49,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:17:49,359] [INFO] Task started: Prodigal
[2023-03-18 05:17:49,359] [INFO] Running command: cat /var/lib/cwl/stgebf4353c-d602-4791-a537-63c497fd3ee4/OceanDNA-b26184.fa | prodigal -d OceanDNA-b26184/cds.fna -a OceanDNA-b26184/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:17:53,916] [INFO] Task succeeded: Prodigal
[2023-03-18 05:17:53,916] [INFO] Task started: HMMsearch
[2023-03-18 05:17:53,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b26184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/reference_markers.hmm OceanDNA-b26184/protein.faa > /dev/null
[2023-03-18 05:17:54,057] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:17:54,058] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebf4353c-d602-4791-a537-63c497fd3ee4/OceanDNA-b26184.fa]
[2023-03-18 05:17:54,070] [INFO] Query marker FASTA was written to OceanDNA-b26184/markers.fasta
[2023-03-18 05:17:54,070] [INFO] Task started: Blastn
[2023-03-18 05:17:54,070] [INFO] Running command: blastn -query OceanDNA-b26184/markers.fasta -db /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/reference_markers.fasta -out OceanDNA-b26184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:17:54,585] [INFO] Task succeeded: Blastn
[2023-03-18 05:17:54,586] [INFO] Selected 21 target genomes.
[2023-03-18 05:17:54,586] [INFO] Target genome list was writen to OceanDNA-b26184/target_genomes.txt
[2023-03-18 05:17:54,599] [INFO] Task started: fastANI
[2023-03-18 05:17:54,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgebf4353c-d602-4791-a537-63c497fd3ee4/OceanDNA-b26184.fa --refList OceanDNA-b26184/target_genomes.txt --output OceanDNA-b26184/fastani_result.tsv --threads 1
[2023-03-18 05:18:07,780] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:07,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:18:07,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:18:07,780] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:18:07,781] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:18:07,781] [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 05:18:07,781] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26184/tc_result.tsv
[2023-03-18 05:18:07,781] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:18:07,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:18:07,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/checkm_data
[2023-03-18 05:18:07,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:18:07,786] [INFO] Task started: CheckM
[2023-03-18 05:18:07,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26184/checkm_input OceanDNA-b26184/checkm_result
[2023-03-18 05:18:26,090] [INFO] Task succeeded: CheckM
[2023-03-18 05:18:26,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 6.89%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-03-18 05:18:26,094] [INFO] ===== Completeness check finished =====
[2023-03-18 05:18:26,094] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:18:26,095] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26184/markers.fasta)
[2023-03-18 05:18:26,095] [INFO] Task started: Blastn
[2023-03-18 05:18:26,095] [INFO] Running command: blastn -query OceanDNA-b26184/markers.fasta -db /var/lib/cwl/stgd73df82d-d13c-4ede-814f-53029c2c15ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:18:26,847] [INFO] Task succeeded: Blastn
[2023-03-18 05:18:26,849] [INFO] Selected 16 target genomes.
[2023-03-18 05:18:26,849] [INFO] Target genome list was writen to OceanDNA-b26184/target_genomes_gtdb.txt
[2023-03-18 05:18:26,899] [INFO] Task started: fastANI
[2023-03-18 05:18:26,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgebf4353c-d602-4791-a537-63c497fd3ee4/OceanDNA-b26184.fa --refList OceanDNA-b26184/target_genomes_gtdb.txt --output OceanDNA-b26184/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:18:32,139] [INFO] Task succeeded: fastANI
[2023-03-18 05:18:32,141] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:18:32,141] [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_018668795.1	s__Puniceispirillum sp018668795	84.7748	93	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	99.26	99.26	0.87	0.87	2	-
GCF_000024465.1	s__Puniceispirillum marinum	83.5277	90	100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:18:32,141] [INFO] GTDB search result was written to OceanDNA-b26184/result_gtdb.tsv
[2023-03-18 05:18:32,141] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:18:32,142] [INFO] DFAST_QC result json was written to OceanDNA-b26184/dqc_result.json
[2023-03-18 05:18:32,142] [INFO] DFAST_QC completed!
[2023-03-18 05:18:32,142] [INFO] Total running time: 0h0m44s