Richard Corbett

I get the same warnings/errors and result when using SAM output (-S).

Running without `-B` or `-S` seems to work without error: `/opt/GenomeWorks-2021.02.2/bin/cudamapper PAG33026_pass_concat.fastq.gz ../hg19a.fa -d 8`

Hi there, I too was trying to run bonito on a multi-GPU machine. I split a folder of fast5s into subfolders once I started to see numbers suggesting it would...

Thanks @seb-mueller, I can confirm that trimmed_repaired_R1.fastq.gz is completely empty. I looked through the logs to try and guess which upstream command creates these files where I see this command:...

I suspect that there is a problem with my fastq format, which I've seen before when using bbMap. My fastq entry names have the following format where there is both...

Used this command: ``` zcat sample1_R1.fastq.gz | sed 's/\/1 / /' | gzip > sample1_R1.fastq_clean.gz zcat sample1_R2.fastq.gz | sed 's/\/2 / /' | gzip > sample1_R2.fastq_clean.gz ``` and am now...

I suspect that not many others are getting read names like ours. I think we have that mix of formats for some backwards compatibility issues in our pipeline and I...

Thanks @Hoohm, I don't seem to have either of those: `find . ./samples ./samples/sample1 ./samples/sample1/top_barcodes.csv ./samples/sample1/barcodes.csv ./samples/sample1/trimmed_repaired_R1.fastq.gz ./samples/sample1/trimmed_repaired_R2.fastq.gz ./samples/sample1/empty_barcode_mapping.pkl ./samples/sample1/barcode_ref.pkl ./samples/sample1/barcode_ext_ref.pkl ./samples/sample1/Log.final.out ./samples/sample1/Log.out ./samples/sample1/_STARtmp find: `./samples/sample1/_STARtmp': Permission denied ./samples/sample1/Log.progress.out ./samples/sample1/read...

The plots folder is there, I think that some plots failed, perhaps due to an R library problem on the server. I do have the plots for the same data...

Hi @Hoohm, Do the plot or data above help you understand how we're only seeing about 3500 reads per cell in our read-based matrix.mtx file? If I understand the plot...