[2023-03-18 20:40:39,454] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,455] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stg567eecf3-00de-486e-9a39-2a1acac8422e/OceanDNA-b22013.fa | prodigal -d OceanDNA-b22013/cds.fna -a OceanDNA-b22013/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:45,713] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:45,714] [INFO] Task started: HMMsearch
[2023-03-18 20:40:45,714] [INFO] Running command: hmmsearch --tblout OceanDNA-b22013/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/reference_markers.hmm OceanDNA-b22013/protein.faa > /dev/null
[2023-03-18 20:40:45,850] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:45,850] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg567eecf3-00de-486e-9a39-2a1acac8422e/OceanDNA-b22013.fa]
[2023-03-18 20:40:45,857] [INFO] Query marker FASTA was written to OceanDNA-b22013/markers.fasta
[2023-03-18 20:40:45,858] [INFO] Task started: Blastn
[2023-03-18 20:40:45,858] [INFO] Running command: blastn -query OceanDNA-b22013/markers.fasta -db /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/reference_markers.fasta -out OceanDNA-b22013/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:47,501] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:47,502] [INFO] Selected 20 target genomes.
[2023-03-18 20:40:47,502] [INFO] Target genome list was writen to OceanDNA-b22013/target_genomes.txt
[2023-03-18 20:40:47,512] [INFO] Task started: fastANI
[2023-03-18 20:40:47,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg567eecf3-00de-486e-9a39-2a1acac8422e/OceanDNA-b22013.fa --refList OceanDNA-b22013/target_genomes.txt --output OceanDNA-b22013/fastani_result.tsv --threads 1
[2023-03-18 20:40:58,537] [INFO] Task succeeded: fastANI
[2023-03-18 20:40:58,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:40:58,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:40:58,538] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:40:58,538] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:40:58,538] [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
--------------------------------------------------------------------------------
[2023-03-18 20:40:58,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22013/tc_result.tsv
[2023-03-18 20:40:58,538] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:40:58,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:40:58,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/checkm_data
[2023-03-18 20:40:58,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:40:58,544] [INFO] Task started: CheckM
[2023-03-18 20:40:58,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22013/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22013/checkm_input OceanDNA-b22013/checkm_result
[2023-03-18 20:41:16,269] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:16,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:16,271] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:16,271] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:16,271] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22013/markers.fasta)
[2023-03-18 20:41:16,271] [INFO] Task started: Blastn
[2023-03-18 20:41:16,271] [INFO] Running command: blastn -query OceanDNA-b22013/markers.fasta -db /var/lib/cwl/stg532aa713-1e8e-4d1e-b32e-65e0b70294aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22013/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:16,730] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:16,730] [INFO] Selected 17 target genomes.
[2023-03-18 20:41:16,731] [INFO] Target genome list was writen to OceanDNA-b22013/target_genomes_gtdb.txt
[2023-03-18 20:41:16,857] [INFO] Task started: fastANI
[2023-03-18 20:41:16,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg567eecf3-00de-486e-9a39-2a1acac8422e/OceanDNA-b22013.fa --refList OceanDNA-b22013/target_genomes_gtdb.txt --output OceanDNA-b22013/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:19,725] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:19,727] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:41:19,727] [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_002331045.1	s__UBA2112 sp002331045	99.6102	215	248	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA2112;g__UBA2112	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 20:41:19,728] [INFO] GTDB search result was written to OceanDNA-b22013/result_gtdb.tsv
[2023-03-18 20:41:19,728] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:19,728] [INFO] DFAST_QC result json was written to OceanDNA-b22013/dqc_result.json
[2023-03-18 20:41:19,728] [INFO] DFAST_QC completed!
[2023-03-18 20:41:19,728] [INFO] Total running time: 0h0m40s