[2023-03-16 13:57:23,576] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:57:23,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:57:23,576] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c0d722-8873-4d18-abf8-4eefd378ba5a/dqc_reference
[2023-03-16 13:57:26,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:57:26,813] [INFO] Task started: Prodigal
[2023-03-16 13:57:26,813] [INFO] Running command: cat /var/lib/cwl/stgf51e47a5-5a0a-4116-9fc1-b29a766ac779/OceanDNA-a4094.fa | prodigal -d OceanDNA-a4094/cds.fna -a OceanDNA-a4094/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:57:34,775] [INFO] Task succeeded: Prodigal
[2023-03-16 13:57:34,775] [INFO] Task started: HMMsearch
[2023-03-16 13:57:34,775] [INFO] Running command: hmmsearch --tblout OceanDNA-a4094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c0d722-8873-4d18-abf8-4eefd378ba5a/dqc_reference/reference_markers.hmm OceanDNA-a4094/protein.faa > /dev/null
[2023-03-16 13:57:35,152] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:57:35,153] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf51e47a5-5a0a-4116-9fc1-b29a766ac779/OceanDNA-a4094.fa]
[2023-03-16 13:57:35,162] [INFO] Query marker FASTA was written to OceanDNA-a4094/markers.fasta
[2023-03-16 13:57:35,163] [INFO] Task started: Blastn
[2023-03-16 13:57:35,163] [INFO] Running command: blastn -query OceanDNA-a4094/markers.fasta -db /var/lib/cwl/stgb3c0d722-8873-4d18-abf8-4eefd378ba5a/dqc_reference/reference_markers.fasta -out OceanDNA-a4094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:57:36,688] [INFO] Task succeeded: Blastn
[2023-03-16 13:57:36,689] [INFO] Selected 0 target genomes.
[2023-03-16 13:57:36,689] [INFO] Target genome list was writen to OceanDNA-a4094/target_genomes.txt
[2023-03-16 13:57:36,689] [ERROR] File is empty. [OceanDNA-a4094/target_genomes.txt]
[2023-03-16 13:57:36,689] [ERROR] Task failed. No target genome found.
[2023-03-16 13:57:36,689] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:57:36,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c0d722-8873-4d18-abf8-4eefd378ba5a/dqc_reference/checkm_data
[2023-03-16 13:57:36,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:57:36,894] [INFO] Task started: CheckM
[2023-03-16 13:57:36,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4094/checkm_input OceanDNA-a4094/checkm_result
[2023-03-16 13:58:12,158] [INFO] Task succeeded: CheckM
[2023-03-16 13:58:12,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.75%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:58:12,159] [INFO] ===== Completeness check finished =====
[2023-03-16 13:58:12,160] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:58:12,160] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4094/markers.fasta)
[2023-03-16 13:58:12,160] [INFO] Task started: Blastn
[2023-03-16 13:58:12,160] [INFO] Running command: blastn -query OceanDNA-a4094/markers.fasta -db /var/lib/cwl/stgb3c0d722-8873-4d18-abf8-4eefd378ba5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:58:12,832] [INFO] Task succeeded: Blastn
[2023-03-16 13:58:12,833] [INFO] Selected 6 target genomes.
[2023-03-16 13:58:12,833] [INFO] Target genome list was writen to OceanDNA-a4094/target_genomes_gtdb.txt
[2023-03-16 13:58:13,004] [INFO] Task started: fastANI
[2023-03-16 13:58:13,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgf51e47a5-5a0a-4116-9fc1-b29a766ac779/OceanDNA-a4094.fa --refList OceanDNA-a4094/target_genomes_gtdb.txt --output OceanDNA-a4094/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:58:14,780] [INFO] Task succeeded: fastANI
[2023-03-16 13:58:14,781] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:58:14,781] [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 13:58:14,781] [INFO] GTDB search result was written to OceanDNA-a4094/result_gtdb.tsv
[2023-03-16 13:58:14,781] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:58:14,781] [INFO] DFAST_QC result json was written to OceanDNA-a4094/dqc_result.json
[2023-03-16 13:58:14,781] [INFO] DFAST_QC completed!
[2023-03-16 13:58:14,782] [INFO] Total running time: 0h0m51s