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s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
https://s4hts.github.io/HTStream/
Apache License 2.0
49 stars 9 forks source link

munmap_chunk(): invalid pointer error #255

Closed jrlyen closed 1 year ago

jrlyen commented 1 year ago

I'm having some problems running HTStream and I'm not sure if there's an issue with my fastq files. I ran the following command: hts_Stats -U 01_A1H_R1_subset.fastq.gz -L stats.json > out.tab and the error I get says: munmap_chunk(): invalid pointer Aborted (core dumped)

I tried hts_Stats on an older fastq file and it works fine suggesting that the installation isn't the problem. I'm running it on Ubuntu 22.04 with version 1.3.2 of htstream

Attached is the fastq file that I used: 01_A1H_R1_subset.fastq.gz

Any insights would be appreciated. I feel like it might be something really simple that I am missing... Thanks!

joe-angell commented 1 year ago

Hi Jeffrey,

This issue is fixed in my open pull request #250, if you want you can try branch bug-stats-249 to get around this issue. I really should merge that pr, it's been over a year ;(.

jrlyen commented 1 year ago

Thanks Joe! In order to run the new code I need to install the program using the git repo right (aka I can't install using "conda install htstream" to get the new updates)? I'm having some trouble with cmake and boost for installation on UC Davis FARM cluster so I reached out to the cluster admin... I tried the fix of using "cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_INCLUDEDIR=/usr/local/include/ .." but it still gives the same error message shown below:

image

I don't think there is anything under the /usr/local/include/ directory though, is there any way I can find where boost is installed (maybe I need to change the path)? I'm loading a module to get the boost package. Maybe there is a simple fix?

joe-angell commented 1 year ago

I'm not terribly familiar with the UC Davis cluster, but you will need to specify the correct path for boost, try:

cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_ROOT=/usr/local ..

If /usr/local doesn't work, you'll need to find the correct path.

joe

On Fri, Jun 23, 2023 at 4:20 PM Jeffrey Yen @.***> wrote:

Thanks Joe! In order to run the new code I need to install the program using the git repo right (aka I can't install using "conda install htstream" to get the new updates)? I'm having some trouble with cmake and boost for installation on UC Davis FARM cluster so I reached out to the cluster admin... I tried the fix of using "cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_INCLUDEDIR=/usr/local/include/ .." but it still gives the same error message shown below: [image: image] https://user-images.githubusercontent.com/55858335/248426426-a349d193-db7d-4669-9ce0-d4a111795919.png I don't think there is anything under the /usr/local/include/ directory though, is there any way I can find where boost is installed (maybe I need to change the path)? I'm loading a module to get the boost package. Maybe there is a simple fix?

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Joe Angell