[2023-03-17 11:36:53,943] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:53,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:53,945] [INFO] DQC Reference Directory: /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference
[2023-03-17 11:36:55,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,047] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,047] [INFO] Running command: cat /var/lib/cwl/stg636251a1-9bf2-4720-be91-ceda229a2976/OceanDNA-b13125.fa | prodigal -d OceanDNA-b13125/cds.fna -a OceanDNA-b13125/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:37:08,335] [INFO] Task succeeded: Prodigal
[2023-03-17 11:37:08,336] [INFO] Task started: HMMsearch
[2023-03-17 11:37:08,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b13125/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/reference_markers.hmm OceanDNA-b13125/protein.faa > /dev/null
[2023-03-17 11:37:08,534] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:37:08,535] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg636251a1-9bf2-4720-be91-ceda229a2976/OceanDNA-b13125.fa]
[2023-03-17 11:37:08,564] [INFO] Query marker FASTA was written to OceanDNA-b13125/markers.fasta
[2023-03-17 11:37:08,565] [INFO] Task started: Blastn
[2023-03-17 11:37:08,565] [INFO] Running command: blastn -query OceanDNA-b13125/markers.fasta -db /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/reference_markers.fasta -out OceanDNA-b13125/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:09,000] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:09,003] [INFO] Selected 19 target genomes.
[2023-03-17 11:37:09,003] [INFO] Target genome list was writen to OceanDNA-b13125/target_genomes.txt
[2023-03-17 11:37:09,017] [INFO] Task started: fastANI
[2023-03-17 11:37:09,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg636251a1-9bf2-4720-be91-ceda229a2976/OceanDNA-b13125.fa --refList OceanDNA-b13125/target_genomes.txt --output OceanDNA-b13125/fastani_result.tsv --threads 1
[2023-03-17 11:37:19,479] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:19,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:19,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:19,480] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:19,480] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:37:19,480] [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
--------------------------------------------------------------------------------
[2023-03-17 11:37:19,482] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13125/tc_result.tsv
[2023-03-17 11:37:19,483] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:19,484] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:19,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/checkm_data
[2023-03-17 11:37:19,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:19,653] [INFO] Task started: CheckM
[2023-03-17 11:37:19,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13125/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13125/checkm_input OceanDNA-b13125/checkm_result
[2023-03-17 11:37:56,823] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:56,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:37:56,846] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:56,846] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:56,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13125/markers.fasta)
[2023-03-17 11:37:56,847] [INFO] Task started: Blastn
[2023-03-17 11:37:56,847] [INFO] Running command: blastn -query OceanDNA-b13125/markers.fasta -db /var/lib/cwl/stgadb28e63-142d-44c0-9c8e-3a2544d7de05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13125/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:57,287] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:57,294] [INFO] Selected 14 target genomes.
[2023-03-17 11:37:57,294] [INFO] Target genome list was writen to OceanDNA-b13125/target_genomes_gtdb.txt
[2023-03-17 11:37:57,307] [INFO] Task started: fastANI
[2023-03-17 11:37:57,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg636251a1-9bf2-4720-be91-ceda229a2976/OceanDNA-b13125.fa --refList OceanDNA-b13125/target_genomes_gtdb.txt --output OceanDNA-b13125/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:38:05,667] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:05,669] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:38:05,669] [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_018649885.1	s__JABIHA01 sp018649885	99.8688	752	762	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__JABIHA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 11:38:05,672] [INFO] GTDB search result was written to OceanDNA-b13125/result_gtdb.tsv
[2023-03-17 11:38:05,677] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:38:05,679] [INFO] DFAST_QC result json was written to OceanDNA-b13125/dqc_result.json
[2023-03-17 11:38:05,679] [INFO] DFAST_QC completed!
[2023-03-17 11:38:05,679] [INFO] Total running time: 0h1m12s