[2023-03-16 09:26:56,832] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:26:56,832] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:26:56,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference
[2023-03-16 09:26:57,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:26:57,902] [INFO] Task started: Prodigal
[2023-03-16 09:26:57,902] [INFO] Running command: cat /var/lib/cwl/stg94612c6d-5908-4462-9b86-009438bccf90/OceanDNA-b25313.fa | prodigal -d OceanDNA-b25313/cds.fna -a OceanDNA-b25313/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:27:00,032] [INFO] Task succeeded: Prodigal
[2023-03-16 09:27:00,032] [INFO] Task started: HMMsearch
[2023-03-16 09:27:00,032] [INFO] Running command: hmmsearch --tblout OceanDNA-b25313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/reference_markers.hmm OceanDNA-b25313/protein.faa > /dev/null
[2023-03-16 09:27:00,146] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:27:00,147] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg94612c6d-5908-4462-9b86-009438bccf90/OceanDNA-b25313.fa]
[2023-03-16 09:27:00,156] [INFO] Query marker FASTA was written to OceanDNA-b25313/markers.fasta
[2023-03-16 09:27:00,157] [INFO] Task started: Blastn
[2023-03-16 09:27:00,157] [INFO] Running command: blastn -query OceanDNA-b25313/markers.fasta -db /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/reference_markers.fasta -out OceanDNA-b25313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:27:00,627] [INFO] Task succeeded: Blastn
[2023-03-16 09:27:00,628] [INFO] Selected 5 target genomes.
[2023-03-16 09:27:00,628] [INFO] Target genome list was writen to OceanDNA-b25313/target_genomes.txt
[2023-03-16 09:27:00,632] [INFO] Task started: fastANI
[2023-03-16 09:27:00,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg94612c6d-5908-4462-9b86-009438bccf90/OceanDNA-b25313.fa --refList OceanDNA-b25313/target_genomes.txt --output OceanDNA-b25313/fastani_result.tsv --threads 1
[2023-03-16 09:27:02,684] [INFO] Task succeeded: fastANI
[2023-03-16 09:27:02,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:27:02,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:27:02,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:27:02,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:27:02,685] [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 09:27:02,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25313/tc_result.tsv
[2023-03-16 09:27:02,685] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:27:02,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:27:02,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/checkm_data
[2023-03-16 09:27:02,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:27:02,697] [INFO] Task started: CheckM
[2023-03-16 09:27:02,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25313/checkm_input OceanDNA-b25313/checkm_result
[2023-03-16 09:27:15,314] [INFO] Task succeeded: CheckM
[2023-03-16 09:27:15,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.27%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:27:15,316] [INFO] ===== Completeness check finished =====
[2023-03-16 09:27:15,316] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:27:15,316] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25313/markers.fasta)
[2023-03-16 09:27:15,317] [INFO] Task started: Blastn
[2023-03-16 09:27:15,317] [INFO] Running command: blastn -query OceanDNA-b25313/markers.fasta -db /var/lib/cwl/stg32157735-06ea-4fba-95d4-d77dd4dfbba9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:27:15,985] [INFO] Task succeeded: Blastn
[2023-03-16 09:27:16,001] [INFO] Selected 11 target genomes.
[2023-03-16 09:27:16,001] [INFO] Target genome list was writen to OceanDNA-b25313/target_genomes_gtdb.txt
[2023-03-16 09:27:16,013] [INFO] Task started: fastANI
[2023-03-16 09:27:16,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg94612c6d-5908-4462-9b86-009438bccf90/OceanDNA-b25313.fa --refList OceanDNA-b25313/target_genomes_gtdb.txt --output OceanDNA-b25313/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:27:17,609] [INFO] Task succeeded: fastANI
[2023-03-16 09:27:17,609] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:27:17,609] [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 09:27:17,619] [INFO] GTDB search result was written to OceanDNA-b25313/result_gtdb.tsv
[2023-03-16 09:27:17,633] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:27:17,647] [INFO] DFAST_QC result json was written to OceanDNA-b25313/dqc_result.json
[2023-03-16 09:27:17,647] [INFO] DFAST_QC completed!
[2023-03-16 09:27:17,647] [INFO] Total running time: 0h0m21s