[2023-03-17 01:44:57,312] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference
[2023-03-17 01:45:00,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:45:00,550] [INFO] Task started: Prodigal
[2023-03-17 01:45:00,550] [INFO] Running command: cat /var/lib/cwl/stgf29e09fc-c00e-471f-b7ca-4658c70d0630/OceanDNA-b43944.fa | prodigal -d OceanDNA-b43944/cds.fna -a OceanDNA-b43944/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:06,477] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:06,478] [INFO] Task started: HMMsearch
[2023-03-17 01:45:06,478] [INFO] Running command: hmmsearch --tblout OceanDNA-b43944/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/reference_markers.hmm OceanDNA-b43944/protein.faa > /dev/null
[2023-03-17 01:45:06,679] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:06,680] [INFO] Found 6/6 markers.
[2023-03-17 01:45:06,691] [INFO] Query marker FASTA was written to OceanDNA-b43944/markers.fasta
[2023-03-17 01:45:06,691] [INFO] Task started: Blastn
[2023-03-17 01:45:06,691] [INFO] Running command: blastn -query OceanDNA-b43944/markers.fasta -db /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/reference_markers.fasta -out OceanDNA-b43944/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:10,093] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:10,093] [INFO] Selected 25 target genomes.
[2023-03-17 01:45:10,094] [INFO] Target genome list was writen to OceanDNA-b43944/target_genomes.txt
[2023-03-17 01:45:10,107] [INFO] Task started: fastANI
[2023-03-17 01:45:10,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29e09fc-c00e-471f-b7ca-4658c70d0630/OceanDNA-b43944.fa --refList OceanDNA-b43944/target_genomes.txt --output OceanDNA-b43944/fastani_result.tsv --threads 1
[2023-03-17 01:45:22,675] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:22,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:22,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:22,676] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:22,676] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:45:22,676] [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
--------------------------------------------------------------------------------
[2023-03-17 01:45:22,676] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43944/tc_result.tsv
[2023-03-17 01:45:22,676] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:22,676] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:22,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/checkm_data
[2023-03-17 01:45:22,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:22,759] [INFO] Task started: CheckM
[2023-03-17 01:45:22,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43944/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43944/checkm_input OceanDNA-b43944/checkm_result
[2023-03-17 01:45:45,983] [INFO] Task succeeded: CheckM
[2023-03-17 01:45:45,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.32%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 01:45:45,985] [INFO] ===== Completeness check finished =====
[2023-03-17 01:45:45,985] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:45:45,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43944/markers.fasta)
[2023-03-17 01:45:45,986] [INFO] Task started: Blastn
[2023-03-17 01:45:45,987] [INFO] Running command: blastn -query OceanDNA-b43944/markers.fasta -db /var/lib/cwl/stg7f1dd6ab-e7db-4bb5-9779-319d6fc77ce9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43944/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:47,132] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:47,133] [INFO] Selected 28 target genomes.
[2023-03-17 01:45:47,133] [INFO] Target genome list was writen to OceanDNA-b43944/target_genomes_gtdb.txt
[2023-03-17 01:45:48,164] [INFO] Task started: fastANI
[2023-03-17 01:45:48,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgf29e09fc-c00e-471f-b7ca-4658c70d0630/OceanDNA-b43944.fa --refList OceanDNA-b43944/target_genomes_gtdb.txt --output OceanDNA-b43944/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:45:58,288] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:58,290] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:45:58,290] [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_018672815.1	s__JABHDX01 sp018672815	83.6734	251	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__JABHDX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:45:58,290] [INFO] GTDB search result was written to OceanDNA-b43944/result_gtdb.tsv
[2023-03-17 01:45:58,290] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:45:58,291] [INFO] DFAST_QC result json was written to OceanDNA-b43944/dqc_result.json
[2023-03-17 01:45:58,291] [INFO] DFAST_QC completed!
[2023-03-17 01:45:58,291] [INFO] Total running time: 0h1m1s