[2023-03-16 19:38:09,843] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:38:09,843] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:38:09,843] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference
[2023-03-16 19:38:10,994] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:38:10,994] [INFO] Task started: Prodigal
[2023-03-16 19:38:10,994] [INFO] Running command: cat /var/lib/cwl/stge24adfca-f7b3-4015-b1f5-39dc35d675ed/OceanDNA-b31520.fa | prodigal -d OceanDNA-b31520/cds.fna -a OceanDNA-b31520/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:38:35,867] [INFO] Task succeeded: Prodigal
[2023-03-16 19:38:35,868] [INFO] Task started: HMMsearch
[2023-03-16 19:38:35,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b31520/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/reference_markers.hmm OceanDNA-b31520/protein.faa > /dev/null
[2023-03-16 19:38:36,056] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:38:36,057] [INFO] Found 6/6 markers.
[2023-03-16 19:38:36,076] [INFO] Query marker FASTA was written to OceanDNA-b31520/markers.fasta
[2023-03-16 19:38:36,077] [INFO] Task started: Blastn
[2023-03-16 19:38:36,077] [INFO] Running command: blastn -query OceanDNA-b31520/markers.fasta -db /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/reference_markers.fasta -out OceanDNA-b31520/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:38:36,669] [INFO] Task succeeded: Blastn
[2023-03-16 19:38:36,670] [INFO] Selected 29 target genomes.
[2023-03-16 19:38:36,671] [INFO] Target genome list was writen to OceanDNA-b31520/target_genomes.txt
[2023-03-16 19:38:36,684] [INFO] Task started: fastANI
[2023-03-16 19:38:36,685] [INFO] Running command: fastANI --query /var/lib/cwl/stge24adfca-f7b3-4015-b1f5-39dc35d675ed/OceanDNA-b31520.fa --refList OceanDNA-b31520/target_genomes.txt --output OceanDNA-b31520/fastani_result.tsv --threads 1
[2023-03-16 19:38:59,673] [INFO] Task succeeded: fastANI
[2023-03-16 19:38:59,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:38:59,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:38:59,677] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:38:59,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:38:59,677] [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
Kordiimonas sediminis	strain=KCTC 42590	GCA_014656395.1	1735581	1735581	type	True	76.1946	53	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:38:59,677] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31520/tc_result.tsv
[2023-03-16 19:38:59,678] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:38:59,678] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:38:59,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/checkm_data
[2023-03-16 19:38:59,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:38:59,733] [INFO] Task started: CheckM
[2023-03-16 19:38:59,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31520/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31520/checkm_input OceanDNA-b31520/checkm_result
[2023-03-16 19:40:04,490] [INFO] Task succeeded: CheckM
[2023-03-16 19:40:04,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:40:04,494] [INFO] ===== Completeness check finished =====
[2023-03-16 19:40:04,494] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:40:04,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31520/markers.fasta)
[2023-03-16 19:40:04,496] [INFO] Task started: Blastn
[2023-03-16 19:40:04,496] [INFO] Running command: blastn -query OceanDNA-b31520/markers.fasta -db /var/lib/cwl/stgb6b35359-764c-4c17-9bcb-191194a9e7e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31520/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:40:05,556] [INFO] Task succeeded: Blastn
[2023-03-16 19:40:05,558] [INFO] Selected 33 target genomes.
[2023-03-16 19:40:05,558] [INFO] Target genome list was writen to OceanDNA-b31520/target_genomes_gtdb.txt
[2023-03-16 19:40:05,622] [INFO] Task started: fastANI
[2023-03-16 19:40:05,622] [INFO] Running command: fastANI --query /var/lib/cwl/stge24adfca-f7b3-4015-b1f5-39dc35d675ed/OceanDNA-b31520.fa --refList OceanDNA-b31520/target_genomes_gtdb.txt --output OceanDNA-b31520/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:40:27,487] [INFO] Task succeeded: fastANI
[2023-03-16 19:40:27,489] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:40:27,489] [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
GCF_014656395.1	s__Kordiimonas sediminis	76.1946	53	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:40:27,489] [INFO] GTDB search result was written to OceanDNA-b31520/result_gtdb.tsv
[2023-03-16 19:40:27,489] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:40:27,490] [INFO] DFAST_QC result json was written to OceanDNA-b31520/dqc_result.json
[2023-03-16 19:40:27,491] [INFO] DFAST_QC completed!
[2023-03-16 19:40:27,491] [INFO] Total running time: 0h2m18s