[2023-03-16 08:22:25,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference
[2023-03-16 08:22:27,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,104] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,104] [INFO] Running command: cat /var/lib/cwl/stgceb8301b-c8c7-403d-a02c-6d719c1fcb65/OceanDNA-b24670.fa | prodigal -d OceanDNA-b24670/cds.fna -a OceanDNA-b24670/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:34,853] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:34,854] [INFO] Task started: HMMsearch
[2023-03-16 08:22:34,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b24670/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/reference_markers.hmm OceanDNA-b24670/protein.faa > /dev/null
[2023-03-16 08:22:35,015] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:35,016] [INFO] Found 6/6 markers.
[2023-03-16 08:22:35,036] [INFO] Query marker FASTA was written to OceanDNA-b24670/markers.fasta
[2023-03-16 08:22:35,038] [INFO] Task started: Blastn
[2023-03-16 08:22:35,038] [INFO] Running command: blastn -query OceanDNA-b24670/markers.fasta -db /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/reference_markers.fasta -out OceanDNA-b24670/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:35,656] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:35,660] [INFO] Selected 27 target genomes.
[2023-03-16 08:22:35,660] [INFO] Target genome list was writen to OceanDNA-b24670/target_genomes.txt
[2023-03-16 08:22:35,675] [INFO] Task started: fastANI
[2023-03-16 08:22:35,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb8301b-c8c7-403d-a02c-6d719c1fcb65/OceanDNA-b24670.fa --refList OceanDNA-b24670/target_genomes.txt --output OceanDNA-b24670/fastani_result.tsv --threads 1
[2023-03-16 08:22:54,211] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:54,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:54,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:54,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:54,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:22:54,212] [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 08:22:54,215] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24670/tc_result.tsv
[2023-03-16 08:22:54,215] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:54,215] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:54,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/checkm_data
[2023-03-16 08:22:54,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:54,225] [INFO] Task started: CheckM
[2023-03-16 08:22:54,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24670/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24670/checkm_input OceanDNA-b24670/checkm_result
[2023-03-16 08:23:19,006] [INFO] Task succeeded: CheckM
[2023-03-16 08:23:19,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:23:19,010] [INFO] ===== Completeness check finished =====
[2023-03-16 08:23:19,010] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:23:19,011] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24670/markers.fasta)
[2023-03-16 08:23:19,012] [INFO] Task started: Blastn
[2023-03-16 08:23:19,012] [INFO] Running command: blastn -query OceanDNA-b24670/markers.fasta -db /var/lib/cwl/stgff9382f4-1ce8-4fd0-8b2f-e01a0c613052/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24670/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:23:20,086] [INFO] Task succeeded: Blastn
[2023-03-16 08:23:20,087] [INFO] Selected 30 target genomes.
[2023-03-16 08:23:20,087] [INFO] Target genome list was writen to OceanDNA-b24670/target_genomes_gtdb.txt
[2023-03-16 08:23:20,146] [INFO] Task started: fastANI
[2023-03-16 08:23:20,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb8301b-c8c7-403d-a02c-6d719c1fcb65/OceanDNA-b24670.fa --refList OceanDNA-b24670/target_genomes_gtdb.txt --output OceanDNA-b24670/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:23:35,846] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:35,848] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:23:35,848] [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
GCA_016184045.1	s__Micavibrio aeruginosavorus_C	76.7737	72	413	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__Micavibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:23:35,849] [INFO] GTDB search result was written to OceanDNA-b24670/result_gtdb.tsv
[2023-03-16 08:23:35,849] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:23:35,850] [INFO] DFAST_QC result json was written to OceanDNA-b24670/dqc_result.json
[2023-03-16 08:23:35,850] [INFO] DFAST_QC completed!
[2023-03-16 08:23:35,850] [INFO] Total running time: 0h1m10s