[2023-03-14 11:33:34,941] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,942] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,950] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference
[2023-03-14 11:33:36,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,265] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,265] [INFO] Running command: cat /var/lib/cwl/stg533edf59-e2fc-4c7e-935f-822681c7c109/OceanDNA-b3654.fa | prodigal -d OceanDNA-b3654/cds.fna -a OceanDNA-b3654/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:34:07,098] [INFO] Task succeeded: Prodigal
[2023-03-14 11:34:07,099] [INFO] Task started: HMMsearch
[2023-03-14 11:34:07,099] [INFO] Running command: hmmsearch --tblout OceanDNA-b3654/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/reference_markers.hmm OceanDNA-b3654/protein.faa > /dev/null
[2023-03-14 11:34:07,374] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:34:07,375] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg533edf59-e2fc-4c7e-935f-822681c7c109/OceanDNA-b3654.fa]
[2023-03-14 11:34:07,408] [INFO] Query marker FASTA was written to OceanDNA-b3654/markers.fasta
[2023-03-14 11:34:07,409] [INFO] Task started: Blastn
[2023-03-14 11:34:07,409] [INFO] Running command: blastn -query OceanDNA-b3654/markers.fasta -db /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/reference_markers.fasta -out OceanDNA-b3654/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:08,005] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:08,005] [INFO] Selected 21 target genomes.
[2023-03-14 11:34:08,006] [INFO] Target genome list was writen to OceanDNA-b3654/target_genomes.txt
[2023-03-14 11:34:08,019] [INFO] Task started: fastANI
[2023-03-14 11:34:08,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg533edf59-e2fc-4c7e-935f-822681c7c109/OceanDNA-b3654.fa --refList OceanDNA-b3654/target_genomes.txt --output OceanDNA-b3654/fastani_result.tsv --threads 1
[2023-03-14 11:34:24,361] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:24,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:24,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:24,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:24,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:34:24,362] [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
--------------------------------------------------------------------------------
[2023-03-14 11:34:24,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3654/tc_result.tsv
[2023-03-14 11:34:24,363] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:24,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:24,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/checkm_data
[2023-03-14 11:34:24,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:24,399] [INFO] Task started: CheckM
[2023-03-14 11:34:24,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3654/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3654/checkm_input OceanDNA-b3654/checkm_result
[2023-03-14 11:35:39,441] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:39,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:39,445] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:39,445] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:39,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3654/markers.fasta)
[2023-03-14 11:35:39,447] [INFO] Task started: Blastn
[2023-03-14 11:35:39,447] [INFO] Running command: blastn -query OceanDNA-b3654/markers.fasta -db /var/lib/cwl/stgcf771b26-2bde-4356-a158-9a4eb23b5730/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3654/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:40,363] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:40,364] [INFO] Selected 27 target genomes.
[2023-03-14 11:35:40,364] [INFO] Target genome list was writen to OceanDNA-b3654/target_genomes_gtdb.txt
[2023-03-14 11:35:40,394] [INFO] Task started: fastANI
[2023-03-14 11:35:40,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg533edf59-e2fc-4c7e-935f-822681c7c109/OceanDNA-b3654.fa --refList OceanDNA-b3654/target_genomes_gtdb.txt --output OceanDNA-b3654/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:36:01,218] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:01,218] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:36:01,218] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:01,218] [INFO] GTDB search result was written to OceanDNA-b3654/result_gtdb.tsv
[2023-03-14 11:36:01,218] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:36:01,219] [INFO] DFAST_QC result json was written to OceanDNA-b3654/dqc_result.json
[2023-03-14 11:36:01,219] [INFO] DFAST_QC completed!
[2023-03-14 11:36:01,219] [INFO] Total running time: 0h2m26s