Rqc aborts with error corrupted double-linked list with valid fastq
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paucarrio ▴ 10
@paucarrio-12170
Last seen 7.1 years ago

Hi,

with package Rqc and a fastq with a single record I get memory errors:

  • corrupted double-linked list
  • memory not mapped

Here a Gist to reproduce the error https://gist.github.com/pauca/f3b843d1939461b8ea2b83ec4b332b04

The Fastq is valid according to fqtools

fqtools validate corrupted.fastq
OK

Thanks for any advice

 

Rqc • 1.1k views
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@wdesouza
Last seen 3.3 years ago
Brazil

Hi paucarrio,

Thank you for sharing this issue. I reproduced your error and I found a bug in internal function of Rqc package. I will fix this error soon as possible. The code below is a workaround for this issue.

library(Rqc)

# replace internal function code to avoid the bug
.readFrequency <- function (chunk)
{
tbl <- table(as.character(sread(chunk)))
count <- as.integer(tbl)
hash <- names(tbl)
data.frame(hash, count, stringsAsFactors = FALSE)
}
assignInNamespace(".readFrequency", .readFrequency, "Rqc")

fs <- "corrupted.fastq"
qa <- rqcQA(fs, sample=F)

 

Best regards,

Welliton
 

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Hi Welliton,

Thanks for the workaround

Pau

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