[2023-03-19 02:20:30,919] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:30,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:30,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference
[2023-03-19 02:20:32,019] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:32,019] [INFO] Task started: Prodigal
[2023-03-19 02:20:32,019] [INFO] Running command: cat /var/lib/cwl/stg8f649c41-68b5-4388-8e2c-ae57a3a8fc48/OceanDNA-b23065.fa | prodigal -d OceanDNA-b23065/cds.fna -a OceanDNA-b23065/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:41,515] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:41,516] [INFO] Task started: HMMsearch
[2023-03-19 02:20:41,516] [INFO] Running command: hmmsearch --tblout OceanDNA-b23065/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/reference_markers.hmm OceanDNA-b23065/protein.faa > /dev/null
[2023-03-19 02:20:41,671] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:41,672] [INFO] Found 6/6 markers.
[2023-03-19 02:20:41,688] [INFO] Query marker FASTA was written to OceanDNA-b23065/markers.fasta
[2023-03-19 02:20:41,690] [INFO] Task started: Blastn
[2023-03-19 02:20:41,690] [INFO] Running command: blastn -query OceanDNA-b23065/markers.fasta -db /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/reference_markers.fasta -out OceanDNA-b23065/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:42,207] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:42,208] [INFO] Selected 13 target genomes.
[2023-03-19 02:20:42,209] [INFO] Target genome list was writen to OceanDNA-b23065/target_genomes.txt
[2023-03-19 02:20:42,217] [INFO] Task started: fastANI
[2023-03-19 02:20:42,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f649c41-68b5-4388-8e2c-ae57a3a8fc48/OceanDNA-b23065.fa --refList OceanDNA-b23065/target_genomes.txt --output OceanDNA-b23065/fastani_result.tsv --threads 1
[2023-03-19 02:20:49,821] [INFO] Task succeeded: fastANI
[2023-03-19 02:20:49,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:20:49,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:20:49,821] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:20:49,822] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:20:49,822] [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 02:20:49,823] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23065/tc_result.tsv
[2023-03-19 02:20:49,824] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:20:49,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:20:49,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/checkm_data
[2023-03-19 02:20:49,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:20:49,832] [INFO] Task started: CheckM
[2023-03-19 02:20:49,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23065/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23065/checkm_input OceanDNA-b23065/checkm_result
[2023-03-19 02:21:18,289] [INFO] Task succeeded: CheckM
[2023-03-19 02:21:18,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:21:18,295] [INFO] ===== Completeness check finished =====
[2023-03-19 02:21:18,296] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:21:18,296] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23065/markers.fasta)
[2023-03-19 02:21:18,297] [INFO] Task started: Blastn
[2023-03-19 02:21:18,297] [INFO] Running command: blastn -query OceanDNA-b23065/markers.fasta -db /var/lib/cwl/stgd3eaa932-0015-4249-8792-f9983903d0ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23065/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:19,037] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:19,040] [INFO] Selected 19 target genomes.
[2023-03-19 02:21:19,040] [INFO] Target genome list was writen to OceanDNA-b23065/target_genomes_gtdb.txt
[2023-03-19 02:21:19,140] [INFO] Task started: fastANI
[2023-03-19 02:21:19,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f649c41-68b5-4388-8e2c-ae57a3a8fc48/OceanDNA-b23065.fa --refList OceanDNA-b23065/target_genomes_gtdb.txt --output OceanDNA-b23065/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:21:28,540] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:28,541] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:21:28,541] [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_002746235.1	s__GCA-2746235 sp002746235	80.7404	308	472	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__GCA-2746235	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:21:28,543] [INFO] GTDB search result was written to OceanDNA-b23065/result_gtdb.tsv
[2023-03-19 02:21:28,544] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:21:28,545] [INFO] DFAST_QC result json was written to OceanDNA-b23065/dqc_result.json
[2023-03-19 02:21:28,545] [INFO] DFAST_QC completed!
[2023-03-19 02:21:28,545] [INFO] Total running time: 0h0m58s