Ka Ming Nip

Can you report your entire log? How many reads are there in total? If you want to assemble 17 transcriptomes for each of 17 input FASTQ files individually, then you...

If you provide multiple FASTQ files to RNA-Bloom in one command, RNA-Bloom will create one assembly. E.g. ``` rnabloom -long reads_01.fastq.gz reads_02.fastq.gz reads_03.fastq.gz ... ``` If you have 3 separate...

Hi @HadrienG , We will make a new release that includes updated pretrained models. For the existing models, this specific environment works for me: `requirements.txt` ``` genometools-genometools htseq=0.11.3 joblib=1.1.0 last...

Hi @nriareal It's hard to say based on the number of reads alone. The key contributor to RNA-Bloom's peak memory usage for short-read assembly is the number of unique k-mers...

I just found out that the segfault has to do with really long CIGAR string in the PAF file. A new PAF file without CIGAR strings has solved the issue...

Hi Robert, The problematic line has 7522 characters and the CIGAR string has 7315 characters after `cg:Z:`. Ka Ming

Yes, I do see noticable difference in my assembly assessment results. Thanks for the reminder. On Thu., Aug. 15, 2019, 7:18 p.m. Joseph Lee, wrote: > Hi @kmnip , >...

Please remove the options `-k 10 -e 5` and try again. If the issue persists, please report the entire log file.

For the first run, the Racon command was killed for some unknown reason. I don't think it has to with memory or the `-k` or `-e` options. The second run...

I found that I only have this issue if the input matrix is wide. No `NegativeArraySizeException` is thrown if the input matrix were transposed from wide to long (using `MatrixOps.transposeSerial(X)`).