Open thierryjanssens opened 2 years ago
Dear Saskia,
I have set the reclustering option as follows (no blastdir, as I use existing blastdb for now):
decona -T 8 -f -l 500 -q 10 -c 0.80 -n 100 -i -g 1 -M -r
The procedure ends without errors (except the one step as in issue #22, which I have solved with a || continue in the problematic step).
Removing previous index file /home/minion/Data_Minion/Proefrun3/fastq_pass/data/unclassified_concatenated/multi-seq/polished_343-1286.fa.fasta.fai Running medaka consensus Using medaka stitch to create consensus. BED delineating regions which were not polished (in draft coordinates): consensus_medaka_343-1286.fa/consensus.fasta.gaps_in_draft_coords.bed Polished assembly written to consensus_medaka_343-1286.fa/consensus.fasta, have a nice day. Done Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode01_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode02_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode03_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode04_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode05_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode06_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode07_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode08_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode09_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode10_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode11_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode12_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/unclassified_concatenated/multi-seq Blast Racon sequences finished
Why doesn't it continue with re-clustering?
kidn regards,
Thierry
Dear Saskia,
I have set the reclustering option as follows (no blastdir, as I use existing blastdb for now):
decona -T 8 -f -l 500 -q 10 -c 0.80 -n 100 -i -g 1 -M -r
The procedure ends without errors (except the one step as in issue #22, which I have solved with a || continue in the problematic step).
Removing previous index file /home/minion/Data_Minion/Proefrun3/fastq_pass/data/unclassified_concatenated/multi-seq/polished_343-1286.fa.fasta.fai Running medaka consensus Using medaka stitch to create consensus. BED delineating regions which were not polished (in draft coordinates): consensus_medaka_343-1286.fa/consensus.fasta.gaps_in_draft_coords.bed Polished assembly written to consensus_medaka_343-1286.fa/consensus.fasta, have a nice day. Done Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode01_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode02_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode03_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode04_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode05_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode06_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode07_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode08_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode09_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode10_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode11_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/barcode12_concatenated/multi-seq Blasting consensus sequences /home/minion/Data_Minion/Proefrun3/fastq_pass/data/unclassified_concatenated/multi-seq Blast Racon sequences finished
Why doesn't it continue with re-clustering?
kidn regards,
Thierry