[2023-03-14 11:33:35,026] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:35,026] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:35,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg44cb23e6-0aee-476c-92c1-53d2ae1f0f30/dqc_reference
[2023-03-14 11:33:36,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,267] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,268] [INFO] Running command: cat /var/lib/cwl/stgd54d7cc2-6068-4bed-86d0-e87195b1b1ff/OceanDNA-a1154.fa | prodigal -d OceanDNA-a1154/cds.fna -a OceanDNA-a1154/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:38,189] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:38,189] [INFO] Task started: HMMsearch
[2023-03-14 11:33:38,189] [INFO] Running command: hmmsearch --tblout OceanDNA-a1154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44cb23e6-0aee-476c-92c1-53d2ae1f0f30/dqc_reference/reference_markers.hmm OceanDNA-a1154/protein.faa > /dev/null
[2023-03-14 11:33:38,316] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:38,317] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd54d7cc2-6068-4bed-86d0-e87195b1b1ff/OceanDNA-a1154.fa]
[2023-03-14 11:33:38,321] [INFO] Query marker FASTA was written to OceanDNA-a1154/markers.fasta
[2023-03-14 11:33:38,323] [INFO] Task started: Blastn
[2023-03-14 11:33:38,323] [INFO] Running command: blastn -query OceanDNA-a1154/markers.fasta -db /var/lib/cwl/stg44cb23e6-0aee-476c-92c1-53d2ae1f0f30/dqc_reference/reference_markers.fasta -out OceanDNA-a1154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:38,775] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:38,775] [INFO] Selected 0 target genomes.
[2023-03-14 11:33:38,776] [INFO] Target genome list was writen to OceanDNA-a1154/target_genomes.txt
[2023-03-14 11:33:38,776] [ERROR] File is empty. [OceanDNA-a1154/target_genomes.txt]
[2023-03-14 11:33:38,776] [ERROR] Task failed. No target genome found.
[2023-03-14 11:33:38,776] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:38,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44cb23e6-0aee-476c-92c1-53d2ae1f0f30/dqc_reference/checkm_data
[2023-03-14 11:33:38,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:38,828] [INFO] Task started: CheckM
[2023-03-14 11:33:38,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1154/checkm_input OceanDNA-a1154/checkm_result
[2023-03-14 11:33:53,082] [INFO] Task succeeded: CheckM
[2023-03-14 11:33:53,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:33:53,083] [INFO] ===== Completeness check finished =====
[2023-03-14 11:33:53,084] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:33:53,084] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1154/markers.fasta)
[2023-03-14 11:33:53,086] [INFO] Task started: Blastn
[2023-03-14 11:33:53,086] [INFO] Running command: blastn -query OceanDNA-a1154/markers.fasta -db /var/lib/cwl/stg44cb23e6-0aee-476c-92c1-53d2ae1f0f30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:53,769] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:53,769] [INFO] Selected 3 target genomes.
[2023-03-14 11:33:53,769] [INFO] Target genome list was writen to OceanDNA-a1154/target_genomes_gtdb.txt
[2023-03-14 11:33:53,774] [INFO] Task started: fastANI
[2023-03-14 11:33:53,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgd54d7cc2-6068-4bed-86d0-e87195b1b1ff/OceanDNA-a1154.fa --refList OceanDNA-a1154/target_genomes_gtdb.txt --output OceanDNA-a1154/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:33:54,195] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:54,197] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:33:54,197] [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_002688325.1	s__ARS1178 sp002688325	99.8562	107	125	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__ARS1178;g__ARS1178	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:33:54,197] [INFO] GTDB search result was written to OceanDNA-a1154/result_gtdb.tsv
[2023-03-14 11:33:54,197] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:33:54,197] [INFO] DFAST_QC result json was written to OceanDNA-a1154/dqc_result.json
[2023-03-14 11:33:54,198] [INFO] DFAST_QC completed!
[2023-03-14 11:33:54,198] [INFO] Total running time: 0h0m19s