[2023-03-17 05:01:06,760] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference
[2023-03-17 05:01:08,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:08,511] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,512] [INFO] Running command: cat /var/lib/cwl/stg56b14cf8-1125-46c2-98e1-630e14f0a089/OceanDNA-b33195.fa | prodigal -d OceanDNA-b33195/cds.fna -a OceanDNA-b33195/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:19,329] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:19,330] [INFO] Task started: HMMsearch
[2023-03-17 05:01:19,330] [INFO] Running command: hmmsearch --tblout OceanDNA-b33195/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/reference_markers.hmm OceanDNA-b33195/protein.faa > /dev/null
[2023-03-17 05:01:19,510] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:19,510] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg56b14cf8-1125-46c2-98e1-630e14f0a089/OceanDNA-b33195.fa]
[2023-03-17 05:01:19,523] [INFO] Query marker FASTA was written to OceanDNA-b33195/markers.fasta
[2023-03-17 05:01:19,523] [INFO] Task started: Blastn
[2023-03-17 05:01:19,523] [INFO] Running command: blastn -query OceanDNA-b33195/markers.fasta -db /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/reference_markers.fasta -out OceanDNA-b33195/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:20,131] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:20,131] [INFO] Selected 29 target genomes.
[2023-03-17 05:01:20,132] [INFO] Target genome list was writen to OceanDNA-b33195/target_genomes.txt
[2023-03-17 05:01:20,151] [INFO] Task started: fastANI
[2023-03-17 05:01:20,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b14cf8-1125-46c2-98e1-630e14f0a089/OceanDNA-b33195.fa --refList OceanDNA-b33195/target_genomes.txt --output OceanDNA-b33195/fastani_result.tsv --threads 1
[2023-03-17 05:01:38,463] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:38,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:38,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:38,464] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:38,464] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:01:38,464] [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 05:01:38,465] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33195/tc_result.tsv
[2023-03-17 05:01:38,465] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:38,465] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:38,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/checkm_data
[2023-03-17 05:01:38,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:38,475] [INFO] Task started: CheckM
[2023-03-17 05:01:38,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33195/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33195/checkm_input OceanDNA-b33195/checkm_result
[2023-03-17 05:02:09,143] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:09,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:09,146] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:09,146] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:09,146] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33195/markers.fasta)
[2023-03-17 05:02:09,146] [INFO] Task started: Blastn
[2023-03-17 05:02:09,146] [INFO] Running command: blastn -query OceanDNA-b33195/markers.fasta -db /var/lib/cwl/stgee8b40c9-b187-44c9-ab47-9f1c7ee4f918/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33195/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:10,178] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:10,179] [INFO] Selected 24 target genomes.
[2023-03-17 05:02:10,179] [INFO] Target genome list was writen to OceanDNA-b33195/target_genomes_gtdb.txt
[2023-03-17 05:02:10,776] [INFO] Task started: fastANI
[2023-03-17 05:02:10,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b14cf8-1125-46c2-98e1-630e14f0a089/OceanDNA-b33195.fa --refList OceanDNA-b33195/target_genomes_gtdb.txt --output OceanDNA-b33195/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:24,974] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:24,976] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:02:24,976] [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_002346425.1	s__UBA3002 sp002346425	99.8452	540	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA3002;g__UBA3002	95.0	99.83	99.83	0.60	0.60	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 05:02:24,976] [INFO] GTDB search result was written to OceanDNA-b33195/result_gtdb.tsv
[2023-03-17 05:02:24,976] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:24,977] [INFO] DFAST_QC result json was written to OceanDNA-b33195/dqc_result.json
[2023-03-17 05:02:24,977] [INFO] DFAST_QC completed!
[2023-03-17 05:02:24,977] [INFO] Total running time: 0h1m18s