[2023-03-19 03:10:00,783] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,783] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference
[2023-03-19 03:10:01,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,897] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,897] [INFO] Running command: cat /var/lib/cwl/stg2fa58c4e-d324-4d27-9631-0d4b1b617bb4/OceanDNA-b38093.fa | prodigal -d OceanDNA-b38093/cds.fna -a OceanDNA-b38093/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:11,243] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:11,243] [INFO] Task started: HMMsearch
[2023-03-19 03:10:11,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b38093/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/reference_markers.hmm OceanDNA-b38093/protein.faa > /dev/null
[2023-03-19 03:10:11,401] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:11,402] [INFO] Found 6/6 markers.
[2023-03-19 03:10:11,417] [INFO] Query marker FASTA was written to OceanDNA-b38093/markers.fasta
[2023-03-19 03:10:11,417] [INFO] Task started: Blastn
[2023-03-19 03:10:11,417] [INFO] Running command: blastn -query OceanDNA-b38093/markers.fasta -db /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/reference_markers.fasta -out OceanDNA-b38093/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:11,971] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:11,972] [INFO] Selected 32 target genomes.
[2023-03-19 03:10:11,972] [INFO] Target genome list was writen to OceanDNA-b38093/target_genomes.txt
[2023-03-19 03:10:11,984] [INFO] Task started: fastANI
[2023-03-19 03:10:11,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa58c4e-d324-4d27-9631-0d4b1b617bb4/OceanDNA-b38093.fa --refList OceanDNA-b38093/target_genomes.txt --output OceanDNA-b38093/fastani_result.tsv --threads 1
[2023-03-19 03:10:31,131] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:31,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:31,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:31,131] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:31,131] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:31,131] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:31,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38093/tc_result.tsv
[2023-03-19 03:10:31,132] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:31,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:31,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/checkm_data
[2023-03-19 03:10:31,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:31,140] [INFO] Task started: CheckM
[2023-03-19 03:10:31,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38093/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38093/checkm_input OceanDNA-b38093/checkm_result
[2023-03-19 03:10:58,880] [INFO] Task succeeded: CheckM
[2023-03-19 03:10:58,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.27%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:10:58,882] [INFO] ===== Completeness check finished =====
[2023-03-19 03:10:58,883] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:10:58,883] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38093/markers.fasta)
[2023-03-19 03:10:58,883] [INFO] Task started: Blastn
[2023-03-19 03:10:58,883] [INFO] Running command: blastn -query OceanDNA-b38093/markers.fasta -db /var/lib/cwl/stg57a7898d-cd9c-4f2d-a116-7bf788b686c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38093/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:59,758] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:59,758] [INFO] Selected 21 target genomes.
[2023-03-19 03:10:59,759] [INFO] Target genome list was writen to OceanDNA-b38093/target_genomes_gtdb.txt
[2023-03-19 03:10:59,794] [INFO] Task started: fastANI
[2023-03-19 03:10:59,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa58c4e-d324-4d27-9631-0d4b1b617bb4/OceanDNA-b38093.fa --refList OceanDNA-b38093/target_genomes_gtdb.txt --output OceanDNA-b38093/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:11,046] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:11,050] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:11,050] [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_002683335.1	s__Luminiphilus sp002683335	98.5886	351	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	conclusive
GCA_016779445.1	s__Luminiphilus sp016779445	93.7645	375	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.89	98.12	0.82	0.77	3	-
GCA_002377985.1	s__Luminiphilus sp002377985	78.3923	210	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081075.1	s__Luminiphilus sp008081075	77.8287	128	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	76.8944	58	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	76.7079	58	484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:11,050] [INFO] GTDB search result was written to OceanDNA-b38093/result_gtdb.tsv
[2023-03-19 03:11:11,050] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:11,051] [INFO] DFAST_QC result json was written to OceanDNA-b38093/dqc_result.json
[2023-03-19 03:11:11,051] [INFO] DFAST_QC completed!
[2023-03-19 03:11:11,051] [INFO] Total running time: 0h1m10s