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comprna / RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
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cannot create std::vector larger than max_size() #14

Open cnk113 opened 4 years ago

cnk113 commented 4 years ago

Hello,

I attempted to run clustering of reads on my fasta reads, but it terminates after a few minutes of starting.


terminate called after throwing an instance of 'std::length_error'
  what():  cannot create std::vector larger than max_size()
Aborted (core dumped)```
ante-turudic commented 3 years ago

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

dedenmatra commented 2 years ago

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

How to produce "clean" input?

ante-turudic commented 2 years ago

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

How to produce "clean" input?

Just remove sequences shorter than kmer size from input file. Lot of tools can do it. I am not sure, but I think used BBtools's reformat.sh script.

dedenmatra commented 2 years ago

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

How to produce "clean" input?

Just remove sequences shorter than kmer size from input file. Lot of tools can do it. I am not sure, but I think used BBtools's reformat.sh script.

I just tried to remove sequences below 200 bp but any criteria for filtering? for example, trimming polyA?

ante-turudic commented 2 years ago

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

How to produce "clean" input?

Just remove sequences shorter than kmer size from input file. Lot of tools can do it. I am not sure, but I think used BBtools's reformat.sh script.

I just tried to remove sequences below 200 bp but any criteria for filtering? for example, trimming polyA?

From my experience no.

EduEyras commented 2 years ago

Thanks for the questions and inputs

We’ll add some info in the README to help with possible issues with the input

Keeping polyA’s should be actually better for clustering and transcript reconstruction

One thing we noticed though is internal adapters in ont cDNA sequencing that will lead to overclustering and need to removed, and the reads must be split

E

On Wed, 13 Oct 2021 at 20:57, Ante Turudic @.***> wrote:

I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size.

How to produce "clean" input?

Just remove sequences shorter than kmer size from input file. Lot of tools can do it. I am not sure, but I think used BBtools's reformat.sh script.

I just tried to remove sequences below 200 bp but any criteria for filtering? for example, trimming polyA?

From my experience no.

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dedenmatra commented 2 years ago

Thanks for the questions and inputs We’ll add some info in the README to help with possible issues with the input Keeping polyA’s should be actually better for clustering and transcript reconstruction One thing we noticed though is internal adapters in ont cDNA sequencing that will lead to overclustering and need to removed, and the reads must be split E On Wed, 13 Oct 2021 at 20:57, Ante Turudic @.***> wrote: I had similar issue, and solution was to 'clean' input file by removing sequences shorter than kmer size. How to produce "clean" input? Just remove sequences shorter than kmer size from input file. Lot of tools can do it. I am not sure, but I think used BBtools's reformat.sh script. I just tried to remove sequences below 200 bp but any criteria for filtering? for example, trimming polyA? From my experience no. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBYQ7LERGUSK3YVDS3LUGVJZFANCNFSM4LXD6H6A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

well, thank for suggestions. I will keep PolyA