[2023-03-16 06:24:06,015] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:24:06,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:24:06,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference
[2023-03-16 06:24:07,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:24:07,106] [INFO] Task started: Prodigal
[2023-03-16 06:24:07,106] [INFO] Running command: cat /var/lib/cwl/stgae7f38e0-ddb2-48f9-8717-92f39f249108/OceanDNA-b21012.fa | prodigal -d OceanDNA-b21012/cds.fna -a OceanDNA-b21012/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:24:20,394] [INFO] Task succeeded: Prodigal
[2023-03-16 06:24:20,394] [INFO] Task started: HMMsearch
[2023-03-16 06:24:20,394] [INFO] Running command: hmmsearch --tblout OceanDNA-b21012/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/reference_markers.hmm OceanDNA-b21012/protein.faa > /dev/null
[2023-03-16 06:24:20,576] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:24:20,576] [INFO] Found 6/6 markers.
[2023-03-16 06:24:20,599] [INFO] Query marker FASTA was written to OceanDNA-b21012/markers.fasta
[2023-03-16 06:24:20,600] [INFO] Task started: Blastn
[2023-03-16 06:24:20,600] [INFO] Running command: blastn -query OceanDNA-b21012/markers.fasta -db /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/reference_markers.fasta -out OceanDNA-b21012/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:21,149] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:21,150] [INFO] Selected 28 target genomes.
[2023-03-16 06:24:21,150] [INFO] Target genome list was writen to OceanDNA-b21012/target_genomes.txt
[2023-03-16 06:24:21,163] [INFO] Task started: fastANI
[2023-03-16 06:24:21,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7f38e0-ddb2-48f9-8717-92f39f249108/OceanDNA-b21012.fa --refList OceanDNA-b21012/target_genomes.txt --output OceanDNA-b21012/fastani_result.tsv --threads 1
[2023-03-16 06:24:43,131] [INFO] Task succeeded: fastANI
[2023-03-16 06:24:43,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:24:43,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:24:43,132] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:24:43,132] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:24:43,132] [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 06:24:43,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21012/tc_result.tsv
[2023-03-16 06:24:43,132] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:24:43,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:24:43,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/checkm_data
[2023-03-16 06:24:43,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:24:43,140] [INFO] Task started: CheckM
[2023-03-16 06:24:43,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21012/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21012/checkm_input OceanDNA-b21012/checkm_result
[2023-03-16 06:25:19,244] [INFO] Task succeeded: CheckM
[2023-03-16 06:25:19,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:25:19,247] [INFO] ===== Completeness check finished =====
[2023-03-16 06:25:19,247] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:25:19,247] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21012/markers.fasta)
[2023-03-16 06:25:19,248] [INFO] Task started: Blastn
[2023-03-16 06:25:19,248] [INFO] Running command: blastn -query OceanDNA-b21012/markers.fasta -db /var/lib/cwl/stg68b83082-da40-44d5-b56a-4034e566edab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21012/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:25:20,022] [INFO] Task succeeded: Blastn
[2023-03-16 06:25:20,023] [INFO] Selected 34 target genomes.
[2023-03-16 06:25:20,023] [INFO] Target genome list was writen to OceanDNA-b21012/target_genomes_gtdb.txt
[2023-03-16 06:25:20,446] [INFO] Task started: fastANI
[2023-03-16 06:25:20,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7f38e0-ddb2-48f9-8717-92f39f249108/OceanDNA-b21012.fa --refList OceanDNA-b21012/target_genomes_gtdb.txt --output OceanDNA-b21012/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:25:43,291] [INFO] Task succeeded: fastANI
[2023-03-16 06:25:43,293] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:25:43,293] [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_016713665.1	s__JADJOR01 sp016713665	76.075	54	658	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	75.6203	53	658	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:25:43,293] [INFO] GTDB search result was written to OceanDNA-b21012/result_gtdb.tsv
[2023-03-16 06:25:43,293] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:25:43,294] [INFO] DFAST_QC result json was written to OceanDNA-b21012/dqc_result.json
[2023-03-16 06:25:43,294] [INFO] DFAST_QC completed!
[2023-03-16 06:25:43,294] [INFO] Total running time: 0h1m37s