Segmentation error while using a tool
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6 weeks ago
Ruqaiya • 0

Hello,

I am using an older version of a tool on WSL and it's showing this when i run my code

smalt index -k 11 -s 1 indexedsmalt12 st22combined_reference.fasta
Segmentation fault

Since this version is not on conda env, i downloaded and extracted on my WSL, and Send it to /bin and set it in the $PATH.

I don't know where I went wrong

smalt • 472 views
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Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why not opt for bwa or any well-maintained tools?

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I am trying to reproduce some bioinformatics data from a research paper-this paper as i was asked to work on an MRSA bioinfo project, so i chose to reproduce data from a research paper instead of coming up with an individual project since im new to the field and i'm working on a laptop which doesnt have a lot of RAM (8GB) and am running out of disk space. And i found out that you have to use similar versions from the paper to be able to reproduce the same result.

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6 weeks ago
Mensur Dlakic ★ 27k

Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of system memory.

You seem to be reproducing some old work using outdated tools, with little experience in this field and with less than ideal computer setup. It seems likely that you will get stuck multiple times and it appears you instantly ask a question about each error, without bothering to check for similar problems. For example, a simple search for segmentation error on this site would tell you that most of them are memory-caused. I think this is a recipe to get frustrated, and I suspect you will quickly wear out the patience of the community here if you keep asking questions about exotic tools. It is a free forum and you are welcome to keep asking questions, but I think they will be ignored if they are of the same variety you have been asking so far.

I will give you an unsolicited advice: 1) try to define your problem better so you are not dealing with outdated tools; 2) use the search function on this website to avoid asking questions for which there are well-known answers; 3) get access to a better computer, specifically with more memory and with a native Linux installation; 4) if possible, get local help.

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Thank you for the advice, i'll keep that in mind.

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