[2023-03-15 17:46:31,748] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference
[2023-03-15 17:46:32,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,863] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,863] [INFO] Running command: cat /var/lib/cwl/stga62c8733-691e-4735-aea4-97aab6794be5/OceanDNA-b26298.fa | prodigal -d OceanDNA-b26298/cds.fna -a OceanDNA-b26298/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:44,921] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:44,921] [INFO] Task started: HMMsearch
[2023-03-15 17:46:44,921] [INFO] Running command: hmmsearch --tblout OceanDNA-b26298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/reference_markers.hmm OceanDNA-b26298/protein.faa > /dev/null
[2023-03-15 17:46:45,092] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:45,092] [INFO] Found 6/6 markers.
[2023-03-15 17:46:45,109] [INFO] Query marker FASTA was written to OceanDNA-b26298/markers.fasta
[2023-03-15 17:46:45,111] [INFO] Task started: Blastn
[2023-03-15 17:46:45,111] [INFO] Running command: blastn -query OceanDNA-b26298/markers.fasta -db /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/reference_markers.fasta -out OceanDNA-b26298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:45,695] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:45,698] [INFO] Selected 23 target genomes.
[2023-03-15 17:46:45,698] [INFO] Target genome list was writen to OceanDNA-b26298/target_genomes.txt
[2023-03-15 17:46:45,716] [INFO] Task started: fastANI
[2023-03-15 17:46:45,716] [INFO] Running command: fastANI --query /var/lib/cwl/stga62c8733-691e-4735-aea4-97aab6794be5/OceanDNA-b26298.fa --refList OceanDNA-b26298/target_genomes.txt --output OceanDNA-b26298/fastani_result.tsv --threads 1
[2023-03-15 17:46:57,143] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:57,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:57,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:57,144] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:57,144] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:57,144] [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 17:46:57,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26298/tc_result.tsv
[2023-03-15 17:46:57,147] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:57,147] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:57,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/checkm_data
[2023-03-15 17:46:57,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:57,154] [INFO] Task started: CheckM
[2023-03-15 17:46:57,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26298/checkm_input OceanDNA-b26298/checkm_result
[2023-03-15 17:47:31,193] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:31,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:31,197] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:31,197] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:31,197] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26298/markers.fasta)
[2023-03-15 17:47:31,199] [INFO] Task started: Blastn
[2023-03-15 17:47:31,199] [INFO] Running command: blastn -query OceanDNA-b26298/markers.fasta -db /var/lib/cwl/stgcb3a25e3-a110-464c-a8bc-d8263f70277d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:32,261] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:32,262] [INFO] Selected 24 target genomes.
[2023-03-15 17:47:32,262] [INFO] Target genome list was writen to OceanDNA-b26298/target_genomes_gtdb.txt
[2023-03-15 17:47:32,287] [INFO] Task started: fastANI
[2023-03-15 17:47:32,287] [INFO] Running command: fastANI --query /var/lib/cwl/stga62c8733-691e-4735-aea4-97aab6794be5/OceanDNA-b26298.fa --refList OceanDNA-b26298/target_genomes_gtdb.txt --output OceanDNA-b26298/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:41,056] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:41,059] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:41,059] [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_002387605.1	s__UBA4588 sp002387605	99.5506	582	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA4588	95.0	99.40	98.72	0.91	0.85	18	conclusive
GCA_002299005.1	s__UBA685 sp002299005	76.7096	62	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780775.1	s__JADHLI01 sp016780775	76.4778	88	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLI01	95.0	99.93	99.93	0.97	0.97	2	-
GCA_011524805.1	s__WTJO01 sp011524805	76.1845	77	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__WTJO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:41,060] [INFO] GTDB search result was written to OceanDNA-b26298/result_gtdb.tsv
[2023-03-15 17:47:41,060] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:41,060] [INFO] DFAST_QC result json was written to OceanDNA-b26298/dqc_result.json
[2023-03-15 17:47:41,060] [INFO] DFAST_QC completed!
[2023-03-15 17:47:41,060] [INFO] Total running time: 0h1m9s