[2023-03-16 20:47:10,616] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:47:10,617] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:47:10,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference
[2023-03-16 20:47:11,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:47:11,752] [INFO] Task started: Prodigal
[2023-03-16 20:47:11,752] [INFO] Running command: cat /var/lib/cwl/stg808f9a0a-ea2e-4347-b6fb-ae5a92e57a5a/OceanDNA-b36751.fa | prodigal -d OceanDNA-b36751/cds.fna -a OceanDNA-b36751/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:47:19,356] [INFO] Task succeeded: Prodigal
[2023-03-16 20:47:19,356] [INFO] Task started: HMMsearch
[2023-03-16 20:47:19,356] [INFO] Running command: hmmsearch --tblout OceanDNA-b36751/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/reference_markers.hmm OceanDNA-b36751/protein.faa > /dev/null
[2023-03-16 20:47:19,530] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:47:19,530] [INFO] Found 6/6 markers.
[2023-03-16 20:47:19,544] [INFO] Query marker FASTA was written to OceanDNA-b36751/markers.fasta
[2023-03-16 20:47:19,545] [INFO] Task started: Blastn
[2023-03-16 20:47:19,545] [INFO] Running command: blastn -query OceanDNA-b36751/markers.fasta -db /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/reference_markers.fasta -out OceanDNA-b36751/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:20,094] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:20,095] [INFO] Selected 14 target genomes.
[2023-03-16 20:47:20,095] [INFO] Target genome list was writen to OceanDNA-b36751/target_genomes.txt
[2023-03-16 20:47:20,103] [INFO] Task started: fastANI
[2023-03-16 20:47:20,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg808f9a0a-ea2e-4347-b6fb-ae5a92e57a5a/OceanDNA-b36751.fa --refList OceanDNA-b36751/target_genomes.txt --output OceanDNA-b36751/fastani_result.tsv --threads 1
[2023-03-16 20:47:27,880] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:27,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:47:27,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:47:27,881] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:47:27,881] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:47:27,881] [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 20:47:27,881] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36751/tc_result.tsv
[2023-03-16 20:47:27,881] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:47:27,881] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:47:27,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/checkm_data
[2023-03-16 20:47:27,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:47:27,988] [INFO] Task started: CheckM
[2023-03-16 20:47:27,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36751/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36751/checkm_input OceanDNA-b36751/checkm_result
[2023-03-16 20:47:52,275] [INFO] Task succeeded: CheckM
[2023-03-16 20:47:52,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.82%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 20:47:52,278] [INFO] ===== Completeness check finished =====
[2023-03-16 20:47:52,278] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:47:52,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36751/markers.fasta)
[2023-03-16 20:47:52,278] [INFO] Task started: Blastn
[2023-03-16 20:47:52,278] [INFO] Running command: blastn -query OceanDNA-b36751/markers.fasta -db /var/lib/cwl/stg02bf6416-9864-4121-bb7a-2b4e463e2694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36751/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:53,192] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:53,193] [INFO] Selected 30 target genomes.
[2023-03-16 20:47:53,193] [INFO] Target genome list was writen to OceanDNA-b36751/target_genomes_gtdb.txt
[2023-03-16 20:47:53,223] [INFO] Task started: fastANI
[2023-03-16 20:47:53,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg808f9a0a-ea2e-4347-b6fb-ae5a92e57a5a/OceanDNA-b36751.fa --refList OceanDNA-b36751/target_genomes_gtdb.txt --output OceanDNA-b36751/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:48:09,441] [INFO] Task succeeded: fastANI
[2023-03-16 20:48:09,444] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:48:09,444] [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_002727775.1	s__UBA4421 sp002727775	97.5023	374	422	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	96.65	95.39	0.75	0.71	4	conclusive
--------------------------------------------------------------------------------
[2023-03-16 20:48:09,444] [INFO] GTDB search result was written to OceanDNA-b36751/result_gtdb.tsv
[2023-03-16 20:48:09,445] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:48:09,445] [INFO] DFAST_QC result json was written to OceanDNA-b36751/dqc_result.json
[2023-03-16 20:48:09,446] [INFO] DFAST_QC completed!
[2023-03-16 20:48:09,446] [INFO] Total running time: 0h0m59s