[2023-03-17 22:37:12,600] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference
[2023-03-17 22:37:14,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,349] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,349] [INFO] Running command: cat /var/lib/cwl/stgc845e648-81f0-45fe-8d1a-1d18da70fc42/OceanDNA-b38114.fa | prodigal -d OceanDNA-b38114/cds.fna -a OceanDNA-b38114/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:25,639] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:25,639] [INFO] Task started: HMMsearch
[2023-03-17 22:37:25,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b38114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/reference_markers.hmm OceanDNA-b38114/protein.faa > /dev/null
[2023-03-17 22:37:25,816] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:25,817] [INFO] Found 6/6 markers.
[2023-03-17 22:37:25,832] [INFO] Query marker FASTA was written to OceanDNA-b38114/markers.fasta
[2023-03-17 22:37:25,833] [INFO] Task started: Blastn
[2023-03-17 22:37:25,833] [INFO] Running command: blastn -query OceanDNA-b38114/markers.fasta -db /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/reference_markers.fasta -out OceanDNA-b38114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:26,379] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:26,380] [INFO] Selected 35 target genomes.
[2023-03-17 22:37:26,381] [INFO] Target genome list was writen to OceanDNA-b38114/target_genomes.txt
[2023-03-17 22:37:26,396] [INFO] Task started: fastANI
[2023-03-17 22:37:26,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgc845e648-81f0-45fe-8d1a-1d18da70fc42/OceanDNA-b38114.fa --refList OceanDNA-b38114/target_genomes.txt --output OceanDNA-b38114/fastani_result.tsv --threads 1
[2023-03-17 22:37:47,778] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:47,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:47,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:47,778] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:47,778] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:37:47,779] [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 22:37:47,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38114/tc_result.tsv
[2023-03-17 22:37:47,779] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:47,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:47,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/checkm_data
[2023-03-17 22:37:47,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:47,786] [INFO] Task started: CheckM
[2023-03-17 22:37:47,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38114/checkm_input OceanDNA-b38114/checkm_result
[2023-03-17 22:38:20,478] [INFO] Task succeeded: CheckM
[2023-03-17 22:38:20,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 22:38:20,481] [INFO] ===== Completeness check finished =====
[2023-03-17 22:38:20,481] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:38:20,481] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38114/markers.fasta)
[2023-03-17 22:38:20,482] [INFO] Task started: Blastn
[2023-03-17 22:38:20,482] [INFO] Running command: blastn -query OceanDNA-b38114/markers.fasta -db /var/lib/cwl/stgfd2b7735-fb37-4722-a3b3-5049b4d3b422/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:38:21,428] [INFO] Task succeeded: Blastn
[2023-03-17 22:38:21,429] [INFO] Selected 27 target genomes.
[2023-03-17 22:38:21,429] [INFO] Target genome list was writen to OceanDNA-b38114/target_genomes_gtdb.txt
[2023-03-17 22:38:21,496] [INFO] Task started: fastANI
[2023-03-17 22:38:21,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgc845e648-81f0-45fe-8d1a-1d18da70fc42/OceanDNA-b38114.fa --refList OceanDNA-b38114/target_genomes_gtdb.txt --output OceanDNA-b38114/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:36,532] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:36,537] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:38:36,537] [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_002689915.1	s__Luminiphilus sp002689915	95.6142	467	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_000227505.4	s__Luminiphilus sp000227505	79.1252	262	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	77.9222	78	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.9109	116	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937065.1	s__Luminiphilus sp009937065	77.7216	91	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	77.3866	99	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:36,537] [INFO] GTDB search result was written to OceanDNA-b38114/result_gtdb.tsv
[2023-03-17 22:38:36,537] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:36,538] [INFO] DFAST_QC result json was written to OceanDNA-b38114/dqc_result.json
[2023-03-17 22:38:36,538] [INFO] DFAST_QC completed!
[2023-03-17 22:38:36,538] [INFO] Total running time: 0h1m24s