[2023-03-18 01:14:00,933] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:14:00,933] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:14:00,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference
[2023-03-18 01:14:02,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:14:02,034] [INFO] Task started: Prodigal
[2023-03-18 01:14:02,034] [INFO] Running command: cat /var/lib/cwl/stg46ecba35-6139-4b6e-b391-d42b09434ab1/OceanDNA-b42838.fa | prodigal -d OceanDNA-b42838/cds.fna -a OceanDNA-b42838/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:05,715] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:05,716] [INFO] Task started: HMMsearch
[2023-03-18 01:14:05,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b42838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/reference_markers.hmm OceanDNA-b42838/protein.faa > /dev/null
[2023-03-18 01:14:05,882] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:05,882] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46ecba35-6139-4b6e-b391-d42b09434ab1/OceanDNA-b42838.fa]
[2023-03-18 01:14:05,890] [INFO] Query marker FASTA was written to OceanDNA-b42838/markers.fasta
[2023-03-18 01:14:05,891] [INFO] Task started: Blastn
[2023-03-18 01:14:05,891] [INFO] Running command: blastn -query OceanDNA-b42838/markers.fasta -db /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/reference_markers.fasta -out OceanDNA-b42838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:06,424] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:06,424] [INFO] Selected 17 target genomes.
[2023-03-18 01:14:06,425] [INFO] Target genome list was writen to OceanDNA-b42838/target_genomes.txt
[2023-03-18 01:14:06,437] [INFO] Task started: fastANI
[2023-03-18 01:14:06,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ecba35-6139-4b6e-b391-d42b09434ab1/OceanDNA-b42838.fa --refList OceanDNA-b42838/target_genomes.txt --output OceanDNA-b42838/fastani_result.tsv --threads 1
[2023-03-18 01:14:16,473] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:16,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:16,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:16,474] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:16,474] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:14:16,474] [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
--------------------------------------------------------------------------------
[2023-03-18 01:14:16,474] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42838/tc_result.tsv
[2023-03-18 01:14:16,474] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:16,474] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:16,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/checkm_data
[2023-03-18 01:14:16,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:16,484] [INFO] Task started: CheckM
[2023-03-18 01:14:16,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42838/checkm_input OceanDNA-b42838/checkm_result
[2023-03-18 01:14:31,954] [INFO] Task succeeded: CheckM
[2023-03-18 01:14:31,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:14:31,956] [INFO] ===== Completeness check finished =====
[2023-03-18 01:14:31,956] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:14:31,956] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42838/markers.fasta)
[2023-03-18 01:14:31,957] [INFO] Task started: Blastn
[2023-03-18 01:14:31,957] [INFO] Running command: blastn -query OceanDNA-b42838/markers.fasta -db /var/lib/cwl/stgbf5c4f89-bc27-4639-822d-016f6cc40781/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:32,596] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:32,596] [INFO] Selected 19 target genomes.
[2023-03-18 01:14:32,597] [INFO] Target genome list was writen to OceanDNA-b42838/target_genomes_gtdb.txt
[2023-03-18 01:14:32,619] [INFO] Task started: fastANI
[2023-03-18 01:14:32,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ecba35-6139-4b6e-b391-d42b09434ab1/OceanDNA-b42838.fa --refList OceanDNA-b42838/target_genomes_gtdb.txt --output OceanDNA-b42838/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:14:38,115] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:38,117] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:14:38,117] [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_015659815.1	s__SZUA-1055 sp015659815	98.2603	181	220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__SZUA-1055	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 01:14:38,117] [INFO] GTDB search result was written to OceanDNA-b42838/result_gtdb.tsv
[2023-03-18 01:14:38,117] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:14:38,118] [INFO] DFAST_QC result json was written to OceanDNA-b42838/dqc_result.json
[2023-03-18 01:14:38,118] [INFO] DFAST_QC completed!
[2023-03-18 01:14:38,118] [INFO] Total running time: 0h0m37s