[2023-03-19 00:33:19,085] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,085] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference
[2023-03-19 00:33:20,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,255] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,255] [INFO] Running command: cat /var/lib/cwl/stg0f35afa8-ca23-4b9a-bc7f-a6c3a5821c84/OceanDNA-b13633.fa | prodigal -d OceanDNA-b13633/cds.fna -a OceanDNA-b13633/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:26,397] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:26,397] [INFO] Task started: HMMsearch
[2023-03-19 00:33:26,397] [INFO] Running command: hmmsearch --tblout OceanDNA-b13633/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/reference_markers.hmm OceanDNA-b13633/protein.faa > /dev/null
[2023-03-19 00:33:26,565] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:26,565] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0f35afa8-ca23-4b9a-bc7f-a6c3a5821c84/OceanDNA-b13633.fa]
[2023-03-19 00:33:26,584] [INFO] Query marker FASTA was written to OceanDNA-b13633/markers.fasta
[2023-03-19 00:33:26,584] [INFO] Task started: Blastn
[2023-03-19 00:33:26,584] [INFO] Running command: blastn -query OceanDNA-b13633/markers.fasta -db /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/reference_markers.fasta -out OceanDNA-b13633/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:27,103] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:27,107] [INFO] Selected 12 target genomes.
[2023-03-19 00:33:27,107] [INFO] Target genome list was writen to OceanDNA-b13633/target_genomes.txt
[2023-03-19 00:33:27,119] [INFO] Task started: fastANI
[2023-03-19 00:33:27,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f35afa8-ca23-4b9a-bc7f-a6c3a5821c84/OceanDNA-b13633.fa --refList OceanDNA-b13633/target_genomes.txt --output OceanDNA-b13633/fastani_result.tsv --threads 1
[2023-03-19 00:33:35,436] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:35,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:35,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:35,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:35,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:35,437] [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
--------------------------------------------------------------------------------
[2023-03-19 00:33:35,467] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13633/tc_result.tsv
[2023-03-19 00:33:35,472] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:35,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:35,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/checkm_data
[2023-03-19 00:33:35,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:35,649] [INFO] Task started: CheckM
[2023-03-19 00:33:35,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13633/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13633/checkm_input OceanDNA-b13633/checkm_result
[2023-03-19 00:33:57,224] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:57,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.48%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:33:57,228] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:57,228] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:57,228] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13633/markers.fasta)
[2023-03-19 00:33:57,228] [INFO] Task started: Blastn
[2023-03-19 00:33:57,228] [INFO] Running command: blastn -query OceanDNA-b13633/markers.fasta -db /var/lib/cwl/stgc5d30575-20f0-4fbd-b43a-f43133864507/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13633/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:57,881] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:57,883] [INFO] Selected 18 target genomes.
[2023-03-19 00:33:57,883] [INFO] Target genome list was writen to OceanDNA-b13633/target_genomes_gtdb.txt
[2023-03-19 00:33:57,910] [INFO] Task started: fastANI
[2023-03-19 00:33:57,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f35afa8-ca23-4b9a-bc7f-a6c3a5821c84/OceanDNA-b13633.fa --refList OceanDNA-b13633/target_genomes_gtdb.txt --output OceanDNA-b13633/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:05,894] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:05,894] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:34:05,894] [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
--------------------------------------------------------------------------------
[2023-03-19 00:34:05,919] [INFO] GTDB search result was written to OceanDNA-b13633/result_gtdb.tsv
[2023-03-19 00:34:05,921] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:05,921] [INFO] DFAST_QC result json was written to OceanDNA-b13633/dqc_result.json
[2023-03-19 00:34:05,921] [INFO] DFAST_QC completed!
[2023-03-19 00:34:05,922] [INFO] Total running time: 0h0m47s