[2023-03-16 17:47:09,006] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:47:09,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:47:09,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference
[2023-03-16 17:47:10,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:47:10,141] [INFO] Task started: Prodigal
[2023-03-16 17:47:10,141] [INFO] Running command: cat /var/lib/cwl/stg4dadf85c-389e-461c-af9c-979f2c1e7e70/OceanDNA-b19755.fa | prodigal -d OceanDNA-b19755/cds.fna -a OceanDNA-b19755/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:47:15,823] [INFO] Task succeeded: Prodigal
[2023-03-16 17:47:15,823] [INFO] Task started: HMMsearch
[2023-03-16 17:47:15,823] [INFO] Running command: hmmsearch --tblout OceanDNA-b19755/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/reference_markers.hmm OceanDNA-b19755/protein.faa > /dev/null
[2023-03-16 17:47:15,963] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:47:15,963] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4dadf85c-389e-461c-af9c-979f2c1e7e70/OceanDNA-b19755.fa]
[2023-03-16 17:47:15,978] [INFO] Query marker FASTA was written to OceanDNA-b19755/markers.fasta
[2023-03-16 17:47:15,980] [INFO] Task started: Blastn
[2023-03-16 17:47:15,980] [INFO] Running command: blastn -query OceanDNA-b19755/markers.fasta -db /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/reference_markers.fasta -out OceanDNA-b19755/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:16,415] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:16,415] [INFO] Selected 6 target genomes.
[2023-03-16 17:47:16,416] [INFO] Target genome list was writen to OceanDNA-b19755/target_genomes.txt
[2023-03-16 17:47:16,420] [INFO] Task started: fastANI
[2023-03-16 17:47:16,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dadf85c-389e-461c-af9c-979f2c1e7e70/OceanDNA-b19755.fa --refList OceanDNA-b19755/target_genomes.txt --output OceanDNA-b19755/fastani_result.tsv --threads 1
[2023-03-16 17:47:19,436] [INFO] Task succeeded: fastANI
[2023-03-16 17:47:19,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:47:19,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:47:19,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:47:19,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:47:19,437] [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 17:47:19,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19755/tc_result.tsv
[2023-03-16 17:47:19,437] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:47:19,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:47:19,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/checkm_data
[2023-03-16 17:47:19,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:47:19,466] [INFO] Task started: CheckM
[2023-03-16 17:47:19,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19755/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19755/checkm_input OceanDNA-b19755/checkm_result
[2023-03-16 17:47:51,466] [INFO] Task succeeded: CheckM
[2023-03-16 17:47:51,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:47:51,468] [INFO] ===== Completeness check finished =====
[2023-03-16 17:47:51,468] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:47:51,469] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19755/markers.fasta)
[2023-03-16 17:47:51,470] [INFO] Task started: Blastn
[2023-03-16 17:47:51,470] [INFO] Running command: blastn -query OceanDNA-b19755/markers.fasta -db /var/lib/cwl/stg06e03da7-7d21-4fd4-a56f-b7cfceb975a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19755/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:51,908] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:51,909] [INFO] Selected 15 target genomes.
[2023-03-16 17:47:51,909] [INFO] Target genome list was writen to OceanDNA-b19755/target_genomes_gtdb.txt
[2023-03-16 17:47:51,925] [INFO] Task started: fastANI
[2023-03-16 17:47:51,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dadf85c-389e-461c-af9c-979f2c1e7e70/OceanDNA-b19755.fa --refList OceanDNA-b19755/target_genomes_gtdb.txt --output OceanDNA-b19755/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:47:56,929] [INFO] Task succeeded: fastANI
[2023-03-16 17:47:56,930] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:47:56,930] [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
--------------------------------------------------------------------------------
[2023-03-16 17:47:56,930] [INFO] GTDB search result was written to OceanDNA-b19755/result_gtdb.tsv
[2023-03-16 17:47:56,930] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:47:56,930] [INFO] DFAST_QC result json was written to OceanDNA-b19755/dqc_result.json
[2023-03-16 17:47:56,931] [INFO] DFAST_QC completed!
[2023-03-16 17:47:56,931] [INFO] Total running time: 0h0m48s