[2023-03-18 08:17:17,729] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference
[2023-03-18 08:17:18,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stga4ae064a-01d6-400a-bbf3-910bb0988e22/OceanDNA-b1863.fa | prodigal -d OceanDNA-b1863/cds.fna -a OceanDNA-b1863/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:22,801] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:22,801] [INFO] Task started: HMMsearch
[2023-03-18 08:17:22,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b1863/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/reference_markers.hmm OceanDNA-b1863/protein.faa > /dev/null
[2023-03-18 08:17:22,969] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:22,970] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga4ae064a-01d6-400a-bbf3-910bb0988e22/OceanDNA-b1863.fa]
[2023-03-18 08:17:22,982] [INFO] Query marker FASTA was written to OceanDNA-b1863/markers.fasta
[2023-03-18 08:17:22,982] [INFO] Task started: Blastn
[2023-03-18 08:17:22,982] [INFO] Running command: blastn -query OceanDNA-b1863/markers.fasta -db /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/reference_markers.fasta -out OceanDNA-b1863/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:23,421] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:23,422] [INFO] Selected 4 target genomes.
[2023-03-18 08:17:23,422] [INFO] Target genome list was writen to OceanDNA-b1863/target_genomes.txt
[2023-03-18 08:17:23,425] [INFO] Task started: fastANI
[2023-03-18 08:17:23,425] [INFO] Running command: fastANI --query /var/lib/cwl/stga4ae064a-01d6-400a-bbf3-910bb0988e22/OceanDNA-b1863.fa --refList OceanDNA-b1863/target_genomes.txt --output OceanDNA-b1863/fastani_result.tsv --threads 1
[2023-03-18 08:17:25,491] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:25,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:25,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:25,492] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:25,492] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:25,492] [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 08:17:25,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1863/tc_result.tsv
[2023-03-18 08:17:25,492] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:25,492] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:25,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/checkm_data
[2023-03-18 08:17:25,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:25,497] [INFO] Task started: CheckM
[2023-03-18 08:17:25,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1863/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1863/checkm_input OceanDNA-b1863/checkm_result
[2023-03-18 08:17:43,259] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:43,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.55%
Contamintation: 1.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:43,261] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:43,261] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:43,261] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1863/markers.fasta)
[2023-03-18 08:17:43,262] [INFO] Task started: Blastn
[2023-03-18 08:17:43,262] [INFO] Running command: blastn -query OceanDNA-b1863/markers.fasta -db /var/lib/cwl/stgff7b0cab-d0bf-4165-8cd4-cad6af87af14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1863/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,692] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,692] [INFO] Selected 9 target genomes.
[2023-03-18 08:17:43,693] [INFO] Target genome list was writen to OceanDNA-b1863/target_genomes_gtdb.txt
[2023-03-18 08:17:43,765] [INFO] Task started: fastANI
[2023-03-18 08:17:43,765] [INFO] Running command: fastANI --query /var/lib/cwl/stga4ae064a-01d6-400a-bbf3-910bb0988e22/OceanDNA-b1863.fa --refList OceanDNA-b1863/target_genomes_gtdb.txt --output OceanDNA-b1863/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:17:46,246] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:46,248] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:17:46,248] [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_002709645.1	s__UBA8592 sp002709645	90.9078	118	131	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:17:46,248] [INFO] GTDB search result was written to OceanDNA-b1863/result_gtdb.tsv
[2023-03-18 08:17:46,248] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:17:46,249] [INFO] DFAST_QC result json was written to OceanDNA-b1863/dqc_result.json
[2023-03-18 08:17:46,249] [INFO] DFAST_QC completed!
[2023-03-18 08:17:46,249] [INFO] Total running time: 0h0m29s