[2023-03-15 10:34:47,888] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stgb842fd4f-be4e-4aed-af4e-983ee00d138f/OceanDNA-b44433.fa | prodigal -d OceanDNA-b44433/cds.fna -a OceanDNA-b44433/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:56,159] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:56,159] [INFO] Task started: HMMsearch
[2023-03-15 10:34:56,159] [INFO] Running command: hmmsearch --tblout OceanDNA-b44433/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/reference_markers.hmm OceanDNA-b44433/protein.faa > /dev/null
[2023-03-15 10:34:56,326] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:56,326] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb842fd4f-be4e-4aed-af4e-983ee00d138f/OceanDNA-b44433.fa]
[2023-03-15 10:34:56,342] [INFO] Query marker FASTA was written to OceanDNA-b44433/markers.fasta
[2023-03-15 10:34:56,342] [INFO] Task started: Blastn
[2023-03-15 10:34:56,342] [INFO] Running command: blastn -query OceanDNA-b44433/markers.fasta -db /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/reference_markers.fasta -out OceanDNA-b44433/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:56,879] [INFO] Task succeeded: Blastn
[2023-03-15 10:34:56,883] [INFO] Selected 7 target genomes.
[2023-03-15 10:34:56,884] [INFO] Target genome list was writen to OceanDNA-b44433/target_genomes.txt
[2023-03-15 10:34:56,887] [INFO] Task started: fastANI
[2023-03-15 10:34:56,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgb842fd4f-be4e-4aed-af4e-983ee00d138f/OceanDNA-b44433.fa --refList OceanDNA-b44433/target_genomes.txt --output OceanDNA-b44433/fastani_result.tsv --threads 1
[2023-03-15 10:35:00,336] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:00,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:00,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:00,336] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:00,336] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:35:00,336] [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 10:35:00,340] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44433/tc_result.tsv
[2023-03-15 10:35:00,340] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:00,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:00,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/checkm_data
[2023-03-15 10:35:00,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:00,350] [INFO] Task started: CheckM
[2023-03-15 10:35:00,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44433/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44433/checkm_input OceanDNA-b44433/checkm_result
[2023-03-15 10:35:23,333] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:23,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:23,537] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:23,537] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:23,537] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44433/markers.fasta)
[2023-03-15 10:35:23,538] [INFO] Task started: Blastn
[2023-03-15 10:35:23,538] [INFO] Running command: blastn -query OceanDNA-b44433/markers.fasta -db /var/lib/cwl/stg86058e93-31b4-4098-9d0f-48517e9ad1f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44433/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:24,441] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:24,445] [INFO] Selected 20 target genomes.
[2023-03-15 10:35:24,445] [INFO] Target genome list was writen to OceanDNA-b44433/target_genomes_gtdb.txt
[2023-03-15 10:35:25,219] [INFO] Task started: fastANI
[2023-03-15 10:35:25,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgb842fd4f-be4e-4aed-af4e-983ee00d138f/OceanDNA-b44433.fa --refList OceanDNA-b44433/target_genomes_gtdb.txt --output OceanDNA-b44433/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:32,998] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:33,000] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:35:33,001] [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_002320385.1	s__UBA7916 sp002320385	99.8022	322	385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA7916;f__UBA7916;g__UBA7916	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 10:35:33,004] [INFO] GTDB search result was written to OceanDNA-b44433/result_gtdb.tsv
[2023-03-15 10:35:33,004] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:33,006] [INFO] DFAST_QC result json was written to OceanDNA-b44433/dqc_result.json
[2023-03-15 10:35:33,007] [INFO] DFAST_QC completed!
[2023-03-15 10:35:33,007] [INFO] Total running time: 0h0m45s