[2023-03-14 12:56:11,125] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:56:11,125] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:56:11,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference
[2023-03-14 12:56:12,242] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:56:12,242] [INFO] Task started: Prodigal
[2023-03-14 12:56:12,242] [INFO] Running command: cat /var/lib/cwl/stgda83ed64-724f-435c-9bfc-72bd124ff380/OceanDNA-b44375.fa | prodigal -d OceanDNA-b44375/cds.fna -a OceanDNA-b44375/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:56:23,206] [INFO] Task succeeded: Prodigal
[2023-03-14 12:56:23,206] [INFO] Task started: HMMsearch
[2023-03-14 12:56:23,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b44375/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/reference_markers.hmm OceanDNA-b44375/protein.faa > /dev/null
[2023-03-14 12:56:23,382] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:56:23,383] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda83ed64-724f-435c-9bfc-72bd124ff380/OceanDNA-b44375.fa]
[2023-03-14 12:56:23,396] [INFO] Query marker FASTA was written to OceanDNA-b44375/markers.fasta
[2023-03-14 12:56:23,398] [INFO] Task started: Blastn
[2023-03-14 12:56:23,398] [INFO] Running command: blastn -query OceanDNA-b44375/markers.fasta -db /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/reference_markers.fasta -out OceanDNA-b44375/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:56:23,987] [INFO] Task succeeded: Blastn
[2023-03-14 12:56:23,987] [INFO] Selected 17 target genomes.
[2023-03-14 12:56:23,988] [INFO] Target genome list was writen to OceanDNA-b44375/target_genomes.txt
[2023-03-14 12:56:24,003] [INFO] Task started: fastANI
[2023-03-14 12:56:24,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgda83ed64-724f-435c-9bfc-72bd124ff380/OceanDNA-b44375.fa --refList OceanDNA-b44375/target_genomes.txt --output OceanDNA-b44375/fastani_result.tsv --threads 1
[2023-03-14 12:56:32,245] [INFO] Task succeeded: fastANI
[2023-03-14 12:56:32,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:56:32,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:56:32,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:56:32,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:56:32,246] [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
--------------------------------------------------------------------------------
[2023-03-14 12:56:32,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44375/tc_result.tsv
[2023-03-14 12:56:32,247] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:56:32,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:56:32,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/checkm_data
[2023-03-14 12:56:32,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:56:32,587] [INFO] Task started: CheckM
[2023-03-14 12:56:32,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44375/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44375/checkm_input OceanDNA-b44375/checkm_result
[2023-03-14 12:57:03,934] [INFO] Task succeeded: CheckM
[2023-03-14 12:57:03,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:57:03,936] [INFO] ===== Completeness check finished =====
[2023-03-14 12:57:03,936] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:57:03,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44375/markers.fasta)
[2023-03-14 12:57:03,938] [INFO] Task started: Blastn
[2023-03-14 12:57:03,938] [INFO] Running command: blastn -query OceanDNA-b44375/markers.fasta -db /var/lib/cwl/stgfe53d494-4a3d-49de-9191-6d1cdb5cdc5b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44375/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:57:05,063] [INFO] Task succeeded: Blastn
[2023-03-14 12:57:05,064] [INFO] Selected 26 target genomes.
[2023-03-14 12:57:05,065] [INFO] Target genome list was writen to OceanDNA-b44375/target_genomes_gtdb.txt
[2023-03-14 12:57:05,087] [INFO] Task started: fastANI
[2023-03-14 12:57:05,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgda83ed64-724f-435c-9bfc-72bd124ff380/OceanDNA-b44375.fa --refList OceanDNA-b44375/target_genomes_gtdb.txt --output OceanDNA-b44375/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:57:18,265] [INFO] Task succeeded: fastANI
[2023-03-14 12:57:18,268] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:57:18,268] [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_002434915.1	s__UBA6522 sp002434915	80.387	422	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__UBA6522	95.0	98.12	97.06	0.85	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:57:18,268] [INFO] GTDB search result was written to OceanDNA-b44375/result_gtdb.tsv
[2023-03-14 12:57:18,268] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:57:18,269] [INFO] DFAST_QC result json was written to OceanDNA-b44375/dqc_result.json
[2023-03-14 12:57:18,269] [INFO] DFAST_QC completed!
[2023-03-14 12:57:18,269] [INFO] Total running time: 0h1m7s