[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,684] [INFO] Running command: cat /var/lib/cwl/stg6534a801-f306-4ca2-b845-26bc5488e741/OceanDNA-b40685.fa | prodigal -d OceanDNA-b40685/cds.fna -a OceanDNA-b40685/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:58,716] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:58,716] [INFO] Task started: HMMsearch
[2023-03-18 20:59:58,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b40685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/reference_markers.hmm OceanDNA-b40685/protein.faa > /dev/null
[2023-03-18 20:59:58,925] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:58,926] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6534a801-f306-4ca2-b845-26bc5488e741/OceanDNA-b40685.fa]
[2023-03-18 20:59:58,950] [INFO] Query marker FASTA was written to OceanDNA-b40685/markers.fasta
[2023-03-18 20:59:58,951] [INFO] Task started: Blastn
[2023-03-18 20:59:58,951] [INFO] Running command: blastn -query OceanDNA-b40685/markers.fasta -db /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/reference_markers.fasta -out OceanDNA-b40685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:59,508] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:59,509] [INFO] Selected 23 target genomes.
[2023-03-18 20:59:59,509] [INFO] Target genome list was writen to OceanDNA-b40685/target_genomes.txt
[2023-03-18 20:59:59,527] [INFO] Task started: fastANI
[2023-03-18 20:59:59,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg6534a801-f306-4ca2-b845-26bc5488e741/OceanDNA-b40685.fa --refList OceanDNA-b40685/target_genomes.txt --output OceanDNA-b40685/fastani_result.tsv --threads 1
[2023-03-18 21:00:14,856] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:14,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:14,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:14,857] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:14,857] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:14,857] [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
--------------------------------------------------------------------------------
[2023-03-18 21:00:14,857] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40685/tc_result.tsv
[2023-03-18 21:00:14,858] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:14,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:14,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/checkm_data
[2023-03-18 21:00:14,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:14,894] [INFO] Task started: CheckM
[2023-03-18 21:00:14,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40685/checkm_input OceanDNA-b40685/checkm_result
[2023-03-18 21:00:51,405] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:51,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:51,417] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:51,417] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:51,417] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40685/markers.fasta)
[2023-03-18 21:00:51,418] [INFO] Task started: Blastn
[2023-03-18 21:00:51,418] [INFO] Running command: blastn -query OceanDNA-b40685/markers.fasta -db /var/lib/cwl/stgf42a2be2-8005-43c4-9db8-52a0359619ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:52,271] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:52,278] [INFO] Selected 21 target genomes.
[2023-03-18 21:00:52,279] [INFO] Target genome list was writen to OceanDNA-b40685/target_genomes_gtdb.txt
[2023-03-18 21:00:52,311] [INFO] Task started: fastANI
[2023-03-18 21:00:52,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg6534a801-f306-4ca2-b845-26bc5488e741/OceanDNA-b40685.fa --refList OceanDNA-b40685/target_genomes_gtdb.txt --output OceanDNA-b40685/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:03,960] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:03,962] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:03,962] [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_009692305.1	s__UBA9145 sp009692305	77.2899	172	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661465.1	s__UBA9145 sp018661465	75.8831	50	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.99	99.98	0.99	0.97	14	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:03,965] [INFO] GTDB search result was written to OceanDNA-b40685/result_gtdb.tsv
[2023-03-18 21:01:03,967] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:03,969] [INFO] DFAST_QC result json was written to OceanDNA-b40685/dqc_result.json
[2023-03-18 21:01:03,969] [INFO] DFAST_QC completed!
[2023-03-18 21:01:03,969] [INFO] Total running time: 0h1m20s