[2023-03-17 11:08:00,430] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,431] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference
[2023-03-17 11:08:01,506] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,507] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,507] [INFO] Running command: cat /var/lib/cwl/stg0af5667e-ac5f-4627-8256-fa572b4bc504/OceanDNA-b35865.fa | prodigal -d OceanDNA-b35865/cds.fna -a OceanDNA-b35865/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:13,804] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:13,804] [INFO] Task started: HMMsearch
[2023-03-17 11:08:13,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b35865/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/reference_markers.hmm OceanDNA-b35865/protein.faa > /dev/null
[2023-03-17 11:08:13,982] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:13,983] [INFO] Found 6/6 markers.
[2023-03-17 11:08:13,998] [INFO] Query marker FASTA was written to OceanDNA-b35865/markers.fasta
[2023-03-17 11:08:13,998] [INFO] Task started: Blastn
[2023-03-17 11:08:13,998] [INFO] Running command: blastn -query OceanDNA-b35865/markers.fasta -db /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/reference_markers.fasta -out OceanDNA-b35865/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:14,558] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:14,559] [INFO] Selected 21 target genomes.
[2023-03-17 11:08:14,560] [INFO] Target genome list was writen to OceanDNA-b35865/target_genomes.txt
[2023-03-17 11:08:14,571] [INFO] Task started: fastANI
[2023-03-17 11:08:14,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg0af5667e-ac5f-4627-8256-fa572b4bc504/OceanDNA-b35865.fa --refList OceanDNA-b35865/target_genomes.txt --output OceanDNA-b35865/fastani_result.tsv --threads 1
[2023-03-17 11:08:23,529] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:23,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:23,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:23,529] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:23,529] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:23,529] [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 11:08:23,530] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35865/tc_result.tsv
[2023-03-17 11:08:23,530] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:23,530] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:23,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/checkm_data
[2023-03-17 11:08:23,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:23,564] [INFO] Task started: CheckM
[2023-03-17 11:08:23,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35865/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35865/checkm_input OceanDNA-b35865/checkm_result
[2023-03-17 11:08:57,635] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:57,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:57,637] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:57,638] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:57,638] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35865/markers.fasta)
[2023-03-17 11:08:57,639] [INFO] Task started: Blastn
[2023-03-17 11:08:57,639] [INFO] Running command: blastn -query OceanDNA-b35865/markers.fasta -db /var/lib/cwl/stg1859b826-fdcf-4bef-b6cf-a1668217d9d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35865/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:58,539] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:58,540] [INFO] Selected 22 target genomes.
[2023-03-17 11:08:58,540] [INFO] Target genome list was writen to OceanDNA-b35865/target_genomes_gtdb.txt
[2023-03-17 11:08:58,881] [INFO] Task started: fastANI
[2023-03-17 11:08:58,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg0af5667e-ac5f-4627-8256-fa572b4bc504/OceanDNA-b35865.fa --refList OceanDNA-b35865/target_genomes_gtdb.txt --output OceanDNA-b35865/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:07,639] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:07,642] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:09:07,642] [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_902551695.1	s__CACJXQ01 sp902551695	97.1182	403	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__CACJXQ01;f__CACJXQ01;g__CACJXQ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902597385.1	s__CACJXQ01 sp902597385	92.6617	516	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__CACJXQ01;f__CACJXQ01;g__CACJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:07,643] [INFO] GTDB search result was written to OceanDNA-b35865/result_gtdb.tsv
[2023-03-17 11:09:07,643] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:07,643] [INFO] DFAST_QC result json was written to OceanDNA-b35865/dqc_result.json
[2023-03-17 11:09:07,643] [INFO] DFAST_QC completed!
[2023-03-17 11:09:07,643] [INFO] Total running time: 0h1m7s