[2023-03-15 18:20:15,201] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:20:15,201] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:20:15,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference
[2023-03-15 18:20:16,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:20:16,845] [INFO] Task started: Prodigal
[2023-03-15 18:20:16,846] [INFO] Running command: cat /var/lib/cwl/stg59cacdbe-45e0-43cb-a6a1-599178ae2f06/OceanDNA-b24226.fa | prodigal -d OceanDNA-b24226/cds.fna -a OceanDNA-b24226/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:20:33,181] [INFO] Task succeeded: Prodigal
[2023-03-15 18:20:33,181] [INFO] Task started: HMMsearch
[2023-03-15 18:20:33,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b24226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/reference_markers.hmm OceanDNA-b24226/protein.faa > /dev/null
[2023-03-15 18:20:33,356] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:20:33,356] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg59cacdbe-45e0-43cb-a6a1-599178ae2f06/OceanDNA-b24226.fa]
[2023-03-15 18:20:33,373] [INFO] Query marker FASTA was written to OceanDNA-b24226/markers.fasta
[2023-03-15 18:20:33,374] [INFO] Task started: Blastn
[2023-03-15 18:20:33,374] [INFO] Running command: blastn -query OceanDNA-b24226/markers.fasta -db /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/reference_markers.fasta -out OceanDNA-b24226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:20:33,910] [INFO] Task succeeded: Blastn
[2023-03-15 18:20:33,911] [INFO] Selected 20 target genomes.
[2023-03-15 18:20:33,911] [INFO] Target genome list was writen to OceanDNA-b24226/target_genomes.txt
[2023-03-15 18:20:34,157] [INFO] Task started: fastANI
[2023-03-15 18:20:34,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg59cacdbe-45e0-43cb-a6a1-599178ae2f06/OceanDNA-b24226.fa --refList OceanDNA-b24226/target_genomes.txt --output OceanDNA-b24226/fastani_result.tsv --threads 1
[2023-03-15 18:20:46,522] [INFO] Task succeeded: fastANI
[2023-03-15 18:20:46,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:20:46,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:20:46,523] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:20:46,523] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:20:46,523] [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
--------------------------------------------------------------------------------
[2023-03-15 18:20:46,523] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24226/tc_result.tsv
[2023-03-15 18:20:46,523] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:20:46,523] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:20:46,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/checkm_data
[2023-03-15 18:20:46,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:20:46,530] [INFO] Task started: CheckM
[2023-03-15 18:20:46,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24226/checkm_input OceanDNA-b24226/checkm_result
[2023-03-15 18:21:29,344] [INFO] Task succeeded: CheckM
[2023-03-15 18:21:29,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:21:29,347] [INFO] ===== Completeness check finished =====
[2023-03-15 18:21:29,347] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:21:29,347] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24226/markers.fasta)
[2023-03-15 18:21:29,349] [INFO] Task started: Blastn
[2023-03-15 18:21:29,349] [INFO] Running command: blastn -query OceanDNA-b24226/markers.fasta -db /var/lib/cwl/stg8f1e1d7e-0581-405b-a17d-406580b25d23/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:21:30,148] [INFO] Task succeeded: Blastn
[2023-03-15 18:21:30,149] [INFO] Selected 25 target genomes.
[2023-03-15 18:21:30,149] [INFO] Target genome list was writen to OceanDNA-b24226/target_genomes_gtdb.txt
[2023-03-15 18:21:30,410] [INFO] Task started: fastANI
[2023-03-15 18:21:30,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg59cacdbe-45e0-43cb-a6a1-599178ae2f06/OceanDNA-b24226.fa --refList OceanDNA-b24226/target_genomes_gtdb.txt --output OceanDNA-b24226/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:21:42,143] [INFO] Task succeeded: fastANI
[2023-03-15 18:21:42,145] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:21:42,145] [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_018666155.1	s__WLXB01 sp018666155	77.2082	125	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__WLXB01	95.0	99.93	99.91	0.96	0.93	5	-
GCA_012103295.1	s__WLXB01 sp012103295	76.4109	98	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__WLXB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:21:42,146] [INFO] GTDB search result was written to OceanDNA-b24226/result_gtdb.tsv
[2023-03-15 18:21:42,146] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:21:42,146] [INFO] DFAST_QC result json was written to OceanDNA-b24226/dqc_result.json
[2023-03-15 18:21:42,146] [INFO] DFAST_QC completed!
[2023-03-15 18:21:42,146] [INFO] Total running time: 0h1m27s