[2023-03-16 10:21:46,939] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:21:46,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:21:46,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference
[2023-03-16 10:21:50,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:21:50,683] [INFO] Task started: Prodigal
[2023-03-16 10:21:50,683] [INFO] Running command: cat /var/lib/cwl/stgaed2547b-0ef4-4c68-8675-9be0fc4387a0/OceanDNA-b22377.fa | prodigal -d OceanDNA-b22377/cds.fna -a OceanDNA-b22377/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:22:06,841] [INFO] Task succeeded: Prodigal
[2023-03-16 10:22:06,841] [INFO] Task started: HMMsearch
[2023-03-16 10:22:06,841] [INFO] Running command: hmmsearch --tblout OceanDNA-b22377/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/reference_markers.hmm OceanDNA-b22377/protein.faa > /dev/null
[2023-03-16 10:22:07,270] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:22:07,270] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaed2547b-0ef4-4c68-8675-9be0fc4387a0/OceanDNA-b22377.fa]
[2023-03-16 10:22:07,334] [INFO] Query marker FASTA was written to OceanDNA-b22377/markers.fasta
[2023-03-16 10:22:07,344] [INFO] Task started: Blastn
[2023-03-16 10:22:07,344] [INFO] Running command: blastn -query OceanDNA-b22377/markers.fasta -db /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/reference_markers.fasta -out OceanDNA-b22377/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:08,317] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:08,318] [INFO] Selected 24 target genomes.
[2023-03-16 10:22:08,318] [INFO] Target genome list was writen to OceanDNA-b22377/target_genomes.txt
[2023-03-16 10:22:08,333] [INFO] Task started: fastANI
[2023-03-16 10:22:08,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgaed2547b-0ef4-4c68-8675-9be0fc4387a0/OceanDNA-b22377.fa --refList OceanDNA-b22377/target_genomes.txt --output OceanDNA-b22377/fastani_result.tsv --threads 1
[2023-03-16 10:22:31,305] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:31,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:22:31,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:22:31,306] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:22:31,306] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:22:31,306] [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 10:22:31,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22377/tc_result.tsv
[2023-03-16 10:22:31,306] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:22:31,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:22:31,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/checkm_data
[2023-03-16 10:22:31,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:22:31,316] [INFO] Task started: CheckM
[2023-03-16 10:22:31,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22377/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22377/checkm_input OceanDNA-b22377/checkm_result
[2023-03-16 10:23:20,060] [INFO] Task succeeded: CheckM
[2023-03-16 10:23:20,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:23:20,126] [INFO] ===== Completeness check finished =====
[2023-03-16 10:23:20,126] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:23:20,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22377/markers.fasta)
[2023-03-16 10:23:20,128] [INFO] Task started: Blastn
[2023-03-16 10:23:20,128] [INFO] Running command: blastn -query OceanDNA-b22377/markers.fasta -db /var/lib/cwl/stg87a5a75c-ee65-4682-a7b6-4f96434f5d82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22377/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:23:21,136] [INFO] Task succeeded: Blastn
[2023-03-16 10:23:21,137] [INFO] Selected 26 target genomes.
[2023-03-16 10:23:21,137] [INFO] Target genome list was writen to OceanDNA-b22377/target_genomes_gtdb.txt
[2023-03-16 10:23:21,371] [INFO] Task started: fastANI
[2023-03-16 10:23:21,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgaed2547b-0ef4-4c68-8675-9be0fc4387a0/OceanDNA-b22377.fa --refList OceanDNA-b22377/target_genomes_gtdb.txt --output OceanDNA-b22377/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:23:47,028] [INFO] Task succeeded: fastANI
[2023-03-16 10:23:47,028] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:23:47,029] [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 10:23:47,029] [INFO] GTDB search result was written to OceanDNA-b22377/result_gtdb.tsv
[2023-03-16 10:23:47,029] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:23:47,029] [INFO] DFAST_QC result json was written to OceanDNA-b22377/dqc_result.json
[2023-03-16 10:23:47,030] [INFO] DFAST_QC completed!
[2023-03-16 10:23:47,030] [INFO] Total running time: 0h2m0s