Robert Vaser
Robert Vaser
Hi Marco, how did you run minimap2? Best regards, Robert
Hello, might be you have insufficient coverage for Racon to polish anything. How many reads are in the fastq file? Only 113 seem to have an alignment with your target...
The dataset you are using has `158590` records, which makes the `113` alignments insufficient for polishing. The dataset has been uploaded at the beginning of 2019 and maybe has too...
I am able to get it running with the following commands: ``` # Overlap phase minimap -Sw5 -m0 -L100 SRR8494940_1.fastq SRR8494940_1.fastq > ovl.paf # Layout phase miniasm -f SRR8494940_1.fastq ovl.paf...
Have you tried running it again to see if it will stall again? Might be a thread deadlock, not sure what to think.
Which racon/minimap2 version are you using? Did you by any chance forgot option `-a` while running minimap2? Invalid file format usually indicates mismatch between the file extension and the file...
Hello, the error might also indicate that an inadequate value has been passed to some memory allocation function. No idea how or what caused it as file parsing went well....
Does this work for you? https://github.com/rvaser/spoa/compare/master...policy Best regards, Robert
Hello Johnathan, sorry for my late reply! It is the number of sequences of the input dataset that were rotated in order to compute the MSA. Best regards, Robert
Hello, can you paste command which produced output.sam? Best regards, Robert