[2023-03-19 02:59:38,438] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference
[2023-03-19 02:59:39,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,528] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,528] [INFO] Running command: cat /var/lib/cwl/stg543f0cc1-3c52-4a8b-a846-543ccaa9bb68/OceanDNA-b43885.fa | prodigal -d OceanDNA-b43885/cds.fna -a OceanDNA-b43885/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:59,009] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:59,009] [INFO] Task started: HMMsearch
[2023-03-19 02:59:59,010] [INFO] Running command: hmmsearch --tblout OceanDNA-b43885/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/reference_markers.hmm OceanDNA-b43885/protein.faa > /dev/null
[2023-03-19 02:59:59,205] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:59,205] [INFO] Found 6/6 markers.
[2023-03-19 02:59:59,229] [INFO] Query marker FASTA was written to OceanDNA-b43885/markers.fasta
[2023-03-19 02:59:59,230] [INFO] Task started: Blastn
[2023-03-19 02:59:59,230] [INFO] Running command: blastn -query OceanDNA-b43885/markers.fasta -db /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/reference_markers.fasta -out OceanDNA-b43885/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:59,807] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:59,809] [INFO] Selected 25 target genomes.
[2023-03-19 02:59:59,809] [INFO] Target genome list was writen to OceanDNA-b43885/target_genomes.txt
[2023-03-19 02:59:59,826] [INFO] Task started: fastANI
[2023-03-19 02:59:59,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg543f0cc1-3c52-4a8b-a846-543ccaa9bb68/OceanDNA-b43885.fa --refList OceanDNA-b43885/target_genomes.txt --output OceanDNA-b43885/fastani_result.tsv --threads 1
[2023-03-19 03:00:13,259] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:13,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:00:13,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:00:13,260] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:00:13,260] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:00:13,260] [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
--------------------------------------------------------------------------------
[2023-03-19 03:00:13,261] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43885/tc_result.tsv
[2023-03-19 03:00:13,262] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:00:13,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:00:13,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/checkm_data
[2023-03-19 03:00:13,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:00:13,272] [INFO] Task started: CheckM
[2023-03-19 03:00:13,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43885/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43885/checkm_input OceanDNA-b43885/checkm_result
[2023-03-19 03:01:02,777] [INFO] Task succeeded: CheckM
[2023-03-19 03:01:02,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:01:02,781] [INFO] ===== Completeness check finished =====
[2023-03-19 03:01:02,781] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:01:02,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43885/markers.fasta)
[2023-03-19 03:01:02,783] [INFO] Task started: Blastn
[2023-03-19 03:01:02,783] [INFO] Running command: blastn -query OceanDNA-b43885/markers.fasta -db /var/lib/cwl/stg0c2abb05-1719-46f0-a98c-5a4a41bcf348/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43885/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:01:03,719] [INFO] Task succeeded: Blastn
[2023-03-19 03:01:03,722] [INFO] Selected 24 target genomes.
[2023-03-19 03:01:03,722] [INFO] Target genome list was writen to OceanDNA-b43885/target_genomes_gtdb.txt
[2023-03-19 03:01:03,744] [INFO] Task started: fastANI
[2023-03-19 03:01:03,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg543f0cc1-3c52-4a8b-a846-543ccaa9bb68/OceanDNA-b43885.fa --refList OceanDNA-b43885/target_genomes_gtdb.txt --output OceanDNA-b43885/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:01:17,385] [INFO] Task succeeded: fastANI
[2023-03-19 03:01:17,387] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:01:17,387] [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_002470515.1	s__Arenicella sp002470515	99.9743	1094	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	99.96	99.91	0.96	0.93	4	conclusive
GCF_003315245.1	s__Arenicella xantha	76.7676	50	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:01:17,388] [INFO] GTDB search result was written to OceanDNA-b43885/result_gtdb.tsv
[2023-03-19 03:01:17,388] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:01:17,390] [INFO] DFAST_QC result json was written to OceanDNA-b43885/dqc_result.json
[2023-03-19 03:01:17,390] [INFO] DFAST_QC completed!
[2023-03-19 03:01:17,390] [INFO] Total running time: 0h1m39s