[2023-03-15 14:06:11,278] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference
[2023-03-15 14:06:12,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,406] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,406] [INFO] Running command: cat /var/lib/cwl/stga39c35a8-71ea-4f18-8bf7-6192e956773c/OceanDNA-b17182.fa | prodigal -d OceanDNA-b17182/cds.fna -a OceanDNA-b17182/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:18,736] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:18,737] [INFO] Task started: HMMsearch
[2023-03-15 14:06:18,737] [INFO] Running command: hmmsearch --tblout OceanDNA-b17182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/reference_markers.hmm OceanDNA-b17182/protein.faa > /dev/null
[2023-03-15 14:06:18,898] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:18,898] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga39c35a8-71ea-4f18-8bf7-6192e956773c/OceanDNA-b17182.fa]
[2023-03-15 14:06:18,912] [INFO] Query marker FASTA was written to OceanDNA-b17182/markers.fasta
[2023-03-15 14:06:18,913] [INFO] Task started: Blastn
[2023-03-15 14:06:18,914] [INFO] Running command: blastn -query OceanDNA-b17182/markers.fasta -db /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/reference_markers.fasta -out OceanDNA-b17182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:19,356] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:19,357] [INFO] Selected 8 target genomes.
[2023-03-15 14:06:19,358] [INFO] Target genome list was writen to OceanDNA-b17182/target_genomes.txt
[2023-03-15 14:06:19,364] [INFO] Task started: fastANI
[2023-03-15 14:06:19,364] [INFO] Running command: fastANI --query /var/lib/cwl/stga39c35a8-71ea-4f18-8bf7-6192e956773c/OceanDNA-b17182.fa --refList OceanDNA-b17182/target_genomes.txt --output OceanDNA-b17182/fastani_result.tsv --threads 1
[2023-03-15 14:06:24,436] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:24,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:24,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:24,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:24,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:06:24,437] [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 14:06:24,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17182/tc_result.tsv
[2023-03-15 14:06:24,438] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:24,438] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:24,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/checkm_data
[2023-03-15 14:06:24,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:24,467] [INFO] Task started: CheckM
[2023-03-15 14:06:24,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17182/checkm_input OceanDNA-b17182/checkm_result
[2023-03-15 14:06:46,272] [INFO] Task succeeded: CheckM
[2023-03-15 14:06:46,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:06:46,275] [INFO] ===== Completeness check finished =====
[2023-03-15 14:06:46,275] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:06:46,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17182/markers.fasta)
[2023-03-15 14:06:46,277] [INFO] Task started: Blastn
[2023-03-15 14:06:46,277] [INFO] Running command: blastn -query OceanDNA-b17182/markers.fasta -db /var/lib/cwl/stg9797ba93-aa77-4498-ad04-c7e05d90bd77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:46,737] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:46,739] [INFO] Selected 9 target genomes.
[2023-03-15 14:06:46,739] [INFO] Target genome list was writen to OceanDNA-b17182/target_genomes_gtdb.txt
[2023-03-15 14:06:46,749] [INFO] Task started: fastANI
[2023-03-15 14:06:46,749] [INFO] Running command: fastANI --query /var/lib/cwl/stga39c35a8-71ea-4f18-8bf7-6192e956773c/OceanDNA-b17182.fa --refList OceanDNA-b17182/target_genomes_gtdb.txt --output OceanDNA-b17182/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:06:51,313] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:51,315] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:06:51,315] [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_018648645.1	s__JABGQS01 sp018648645	99.9674	229	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__SZUA-584;g__JABGQS01	95.0	99.94	99.94	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 14:06:51,316] [INFO] GTDB search result was written to OceanDNA-b17182/result_gtdb.tsv
[2023-03-15 14:06:51,316] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:06:51,317] [INFO] DFAST_QC result json was written to OceanDNA-b17182/dqc_result.json
[2023-03-15 14:06:51,317] [INFO] DFAST_QC completed!
[2023-03-15 14:06:51,317] [INFO] Total running time: 0h0m40s