[2023-03-16 17:54:39,802] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:54:39,802] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:54:39,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference
[2023-03-16 17:54:42,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:54:42,645] [INFO] Task started: Prodigal
[2023-03-16 17:54:42,646] [INFO] Running command: cat /var/lib/cwl/stg78a73086-f553-4490-a291-a8c27c20f774/OceanDNA-b35458.fa | prodigal -d OceanDNA-b35458/cds.fna -a OceanDNA-b35458/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:54:48,569] [INFO] Task succeeded: Prodigal
[2023-03-16 17:54:48,570] [INFO] Task started: HMMsearch
[2023-03-16 17:54:48,570] [INFO] Running command: hmmsearch --tblout OceanDNA-b35458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/reference_markers.hmm OceanDNA-b35458/protein.faa > /dev/null
[2023-03-16 17:54:48,757] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:54:48,758] [INFO] Found 6/6 markers.
[2023-03-16 17:54:48,766] [INFO] Query marker FASTA was written to OceanDNA-b35458/markers.fasta
[2023-03-16 17:54:48,767] [INFO] Task started: Blastn
[2023-03-16 17:54:48,767] [INFO] Running command: blastn -query OceanDNA-b35458/markers.fasta -db /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/reference_markers.fasta -out OceanDNA-b35458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:54:49,341] [INFO] Task succeeded: Blastn
[2023-03-16 17:54:49,342] [INFO] Selected 17 target genomes.
[2023-03-16 17:54:49,342] [INFO] Target genome list was writen to OceanDNA-b35458/target_genomes.txt
[2023-03-16 17:54:49,355] [INFO] Task started: fastANI
[2023-03-16 17:54:49,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a73086-f553-4490-a291-a8c27c20f774/OceanDNA-b35458.fa --refList OceanDNA-b35458/target_genomes.txt --output OceanDNA-b35458/fastani_result.tsv --threads 1
[2023-03-16 17:54:57,538] [INFO] Task succeeded: fastANI
[2023-03-16 17:54:57,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:54:57,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:54:57,539] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:54:57,539] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:54:57,539] [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 17:54:57,540] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35458/tc_result.tsv
[2023-03-16 17:54:57,540] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:54:57,540] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:54:57,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/checkm_data
[2023-03-16 17:54:57,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:54:57,545] [INFO] Task started: CheckM
[2023-03-16 17:54:57,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35458/checkm_input OceanDNA-b35458/checkm_result
[2023-03-16 17:55:18,422] [INFO] Task succeeded: CheckM
[2023-03-16 17:55:18,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:55:18,429] [INFO] ===== Completeness check finished =====
[2023-03-16 17:55:18,429] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:55:18,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35458/markers.fasta)
[2023-03-16 17:55:18,431] [INFO] Task started: Blastn
[2023-03-16 17:55:18,431] [INFO] Running command: blastn -query OceanDNA-b35458/markers.fasta -db /var/lib/cwl/stg7590dbf5-0095-4a8b-b854-c4aa5c175df8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:55:20,872] [INFO] Task succeeded: Blastn
[2023-03-16 17:55:20,874] [INFO] Selected 22 target genomes.
[2023-03-16 17:55:20,875] [INFO] Target genome list was writen to OceanDNA-b35458/target_genomes_gtdb.txt
[2023-03-16 17:55:20,903] [INFO] Task started: fastANI
[2023-03-16 17:55:20,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg78a73086-f553-4490-a291-a8c27c20f774/OceanDNA-b35458.fa --refList OceanDNA-b35458/target_genomes_gtdb.txt --output OceanDNA-b35458/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:55:29,714] [INFO] Task succeeded: fastANI
[2023-03-16 17:55:29,718] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:55:29,718] [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_018675635.1	s__GCA-2705445 sp018675635	99.9821	268	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCA_018674175.1	s__GCA-2705445 sp018674175	77.9767	155	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	99.85	99.83	0.95	0.93	3	-
GCA_002705445.1	s__GCA-2705445 sp002705445	77.5648	97	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	97.03	97.03	0.89	0.89	2	-
GCA_902624655.1	s__GCA-2705445 sp902624655	76.9049	94	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:55:29,719] [INFO] GTDB search result was written to OceanDNA-b35458/result_gtdb.tsv
[2023-03-16 17:55:29,720] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:55:29,721] [INFO] DFAST_QC result json was written to OceanDNA-b35458/dqc_result.json
[2023-03-16 17:55:29,721] [INFO] DFAST_QC completed!
[2023-03-16 17:55:29,721] [INFO] Total running time: 0h0m50s