[2023-03-18 01:59:39,762] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,763] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,763] [INFO] DQC Reference Directory: /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference
[2023-03-18 01:59:40,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,954] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,954] [INFO] Running command: cat /var/lib/cwl/stgd5b3b6f0-0519-42df-beb4-a24d705958ea/OceanDNA-b21059.fa | prodigal -d OceanDNA-b21059/cds.fna -a OceanDNA-b21059/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:48,388] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:48,389] [INFO] Task started: HMMsearch
[2023-03-18 01:59:48,389] [INFO] Running command: hmmsearch --tblout OceanDNA-b21059/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/reference_markers.hmm OceanDNA-b21059/protein.faa > /dev/null
[2023-03-18 01:59:48,571] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:48,571] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd5b3b6f0-0519-42df-beb4-a24d705958ea/OceanDNA-b21059.fa]
[2023-03-18 01:59:48,605] [INFO] Query marker FASTA was written to OceanDNA-b21059/markers.fasta
[2023-03-18 01:59:48,606] [INFO] Task started: Blastn
[2023-03-18 01:59:48,606] [INFO] Running command: blastn -query OceanDNA-b21059/markers.fasta -db /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/reference_markers.fasta -out OceanDNA-b21059/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:49,147] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:49,150] [INFO] Selected 18 target genomes.
[2023-03-18 01:59:49,151] [INFO] Target genome list was writen to OceanDNA-b21059/target_genomes.txt
[2023-03-18 01:59:49,162] [INFO] Task started: fastANI
[2023-03-18 01:59:49,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b3b6f0-0519-42df-beb4-a24d705958ea/OceanDNA-b21059.fa --refList OceanDNA-b21059/target_genomes.txt --output OceanDNA-b21059/fastani_result.tsv --threads 1
[2023-03-18 02:00:00,450] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:00,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:00,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:00,451] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:00,451] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:00:00,451] [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 02:00:00,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21059/tc_result.tsv
[2023-03-18 02:00:00,453] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:00,453] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:00,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/checkm_data
[2023-03-18 02:00:00,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:00,468] [INFO] Task started: CheckM
[2023-03-18 02:00:00,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21059/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21059/checkm_input OceanDNA-b21059/checkm_result
[2023-03-18 02:00:24,626] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:24,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.91%
Contamintation: 2.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:24,652] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:24,652] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:24,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21059/markers.fasta)
[2023-03-18 02:00:24,654] [INFO] Task started: Blastn
[2023-03-18 02:00:24,654] [INFO] Running command: blastn -query OceanDNA-b21059/markers.fasta -db /var/lib/cwl/stgc32bf7f7-7934-4704-ad62-bf68e9a7c15f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21059/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:25,531] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:25,536] [INFO] Selected 26 target genomes.
[2023-03-18 02:00:25,536] [INFO] Target genome list was writen to OceanDNA-b21059/target_genomes_gtdb.txt
[2023-03-18 02:00:25,644] [INFO] Task started: fastANI
[2023-03-18 02:00:25,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b3b6f0-0519-42df-beb4-a24d705958ea/OceanDNA-b21059.fa --refList OceanDNA-b21059/target_genomes_gtdb.txt --output OceanDNA-b21059/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:38,988] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:38,988] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:00:38,988] [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
--------------------------------------------------------------------------------
[2023-03-18 02:00:38,990] [INFO] GTDB search result was written to OceanDNA-b21059/result_gtdb.tsv
[2023-03-18 02:00:38,993] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:38,996] [INFO] DFAST_QC result json was written to OceanDNA-b21059/dqc_result.json
[2023-03-18 02:00:38,996] [INFO] DFAST_QC completed!
[2023-03-18 02:00:38,996] [INFO] Total running time: 0h0m59s