[2023-03-17 05:10:04,756] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference
[2023-03-17 05:10:05,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:05,937] [INFO] Task started: Prodigal
[2023-03-17 05:10:05,937] [INFO] Running command: cat /var/lib/cwl/stg0c8d16f1-c36d-4470-8e0f-5efc17b8131a/OceanDNA-b45310.fa | prodigal -d OceanDNA-b45310/cds.fna -a OceanDNA-b45310/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:13,235] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:13,236] [INFO] Task started: HMMsearch
[2023-03-17 05:10:13,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b45310/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/reference_markers.hmm OceanDNA-b45310/protein.faa > /dev/null
[2023-03-17 05:10:13,397] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:13,397] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0c8d16f1-c36d-4470-8e0f-5efc17b8131a/OceanDNA-b45310.fa]
[2023-03-17 05:10:13,405] [INFO] Query marker FASTA was written to OceanDNA-b45310/markers.fasta
[2023-03-17 05:10:13,406] [INFO] Task started: Blastn
[2023-03-17 05:10:13,406] [INFO] Running command: blastn -query OceanDNA-b45310/markers.fasta -db /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/reference_markers.fasta -out OceanDNA-b45310/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:13,892] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:13,892] [INFO] Selected 8 target genomes.
[2023-03-17 05:10:13,893] [INFO] Target genome list was writen to OceanDNA-b45310/target_genomes.txt
[2023-03-17 05:10:13,898] [INFO] Task started: fastANI
[2023-03-17 05:10:13,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c8d16f1-c36d-4470-8e0f-5efc17b8131a/OceanDNA-b45310.fa --refList OceanDNA-b45310/target_genomes.txt --output OceanDNA-b45310/fastani_result.tsv --threads 1
[2023-03-17 05:10:17,000] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:17,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:17,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:17,001] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:17,001] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:10:17,001] [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 05:10:17,001] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45310/tc_result.tsv
[2023-03-17 05:10:17,002] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:17,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:17,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/checkm_data
[2023-03-17 05:10:17,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:17,025] [INFO] Task started: CheckM
[2023-03-17 05:10:17,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45310/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45310/checkm_input OceanDNA-b45310/checkm_result
[2023-03-17 05:10:41,120] [INFO] Task succeeded: CheckM
[2023-03-17 05:10:41,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:10:41,122] [INFO] ===== Completeness check finished =====
[2023-03-17 05:10:41,122] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:10:41,122] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45310/markers.fasta)
[2023-03-17 05:10:41,123] [INFO] Task started: Blastn
[2023-03-17 05:10:41,123] [INFO] Running command: blastn -query OceanDNA-b45310/markers.fasta -db /var/lib/cwl/stg5c47a6bf-5eb3-4e8d-a863-460283cf42fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45310/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:41,780] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:41,781] [INFO] Selected 20 target genomes.
[2023-03-17 05:10:41,781] [INFO] Target genome list was writen to OceanDNA-b45310/target_genomes_gtdb.txt
[2023-03-17 05:10:41,991] [INFO] Task started: fastANI
[2023-03-17 05:10:41,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c8d16f1-c36d-4470-8e0f-5efc17b8131a/OceanDNA-b45310.fa --refList OceanDNA-b45310/target_genomes_gtdb.txt --output OceanDNA-b45310/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:10:47,008] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:47,010] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:10:47,010] [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_002501535.1	s__UBA6624 sp002501535	78.545	135	329	d__Bacteria;p__UBP7;c__UBA6624;o__UBA6624;f__UBA6624;g__UBA6624	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:10:47,011] [INFO] GTDB search result was written to OceanDNA-b45310/result_gtdb.tsv
[2023-03-17 05:10:47,011] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:10:47,011] [INFO] DFAST_QC result json was written to OceanDNA-b45310/dqc_result.json
[2023-03-17 05:10:47,011] [INFO] DFAST_QC completed!
[2023-03-17 05:10:47,011] [INFO] Total running time: 0h0m42s