[2023-03-16 02:38:04,619] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference
[2023-03-16 02:38:05,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:05,901] [INFO] Task started: Prodigal
[2023-03-16 02:38:05,901] [INFO] Running command: cat /var/lib/cwl/stg10b1d6f0-4e4e-4d79-9cf5-56b8bb43d830/OceanDNA-b43437.fa | prodigal -d OceanDNA-b43437/cds.fna -a OceanDNA-b43437/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:17,455] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:17,455] [INFO] Task started: HMMsearch
[2023-03-16 02:38:17,455] [INFO] Running command: hmmsearch --tblout OceanDNA-b43437/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/reference_markers.hmm OceanDNA-b43437/protein.faa > /dev/null
[2023-03-16 02:38:17,625] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:17,625] [INFO] Found 6/6 markers.
[2023-03-16 02:38:17,639] [INFO] Query marker FASTA was written to OceanDNA-b43437/markers.fasta
[2023-03-16 02:38:17,639] [INFO] Task started: Blastn
[2023-03-16 02:38:17,639] [INFO] Running command: blastn -query OceanDNA-b43437/markers.fasta -db /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/reference_markers.fasta -out OceanDNA-b43437/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:18,181] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:18,182] [INFO] Selected 18 target genomes.
[2023-03-16 02:38:18,182] [INFO] Target genome list was writen to OceanDNA-b43437/target_genomes.txt
[2023-03-16 02:38:18,192] [INFO] Task started: fastANI
[2023-03-16 02:38:18,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b1d6f0-4e4e-4d79-9cf5-56b8bb43d830/OceanDNA-b43437.fa --refList OceanDNA-b43437/target_genomes.txt --output OceanDNA-b43437/fastani_result.tsv --threads 1
[2023-03-16 02:38:29,020] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:29,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:29,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:29,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:29,021] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:29,021] [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
--------------------------------------------------------------------------------
[2023-03-16 02:38:29,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43437/tc_result.tsv
[2023-03-16 02:38:29,021] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:29,021] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:29,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/checkm_data
[2023-03-16 02:38:29,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:29,030] [INFO] Task started: CheckM
[2023-03-16 02:38:29,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43437/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43437/checkm_input OceanDNA-b43437/checkm_result
[2023-03-16 02:39:01,327] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:01,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:01,329] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:01,329] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:01,330] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43437/markers.fasta)
[2023-03-16 02:39:01,330] [INFO] Task started: Blastn
[2023-03-16 02:39:01,330] [INFO] Running command: blastn -query OceanDNA-b43437/markers.fasta -db /var/lib/cwl/stgceaa6fcd-de1f-4815-a528-8f0cfeeaf13f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43437/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:02,179] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:02,179] [INFO] Selected 24 target genomes.
[2023-03-16 02:39:02,179] [INFO] Target genome list was writen to OceanDNA-b43437/target_genomes_gtdb.txt
[2023-03-16 02:39:02,666] [INFO] Task started: fastANI
[2023-03-16 02:39:02,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b1d6f0-4e4e-4d79-9cf5-56b8bb43d830/OceanDNA-b43437.fa --refList OceanDNA-b43437/target_genomes_gtdb.txt --output OceanDNA-b43437/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:15,438] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:15,440] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:15,440] [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_002724185.1	s__GCA-2724185 sp002724185	99.942	679	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2724185	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-16 02:39:15,440] [INFO] GTDB search result was written to OceanDNA-b43437/result_gtdb.tsv
[2023-03-16 02:39:15,440] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:15,441] [INFO] DFAST_QC result json was written to OceanDNA-b43437/dqc_result.json
[2023-03-16 02:39:15,441] [INFO] DFAST_QC completed!
[2023-03-16 02:39:15,441] [INFO] Total running time: 0h1m11s