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JY-Zhou / FreePSI

An alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
GNU General Public License v3.0
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Segmentation fault (core dumped) #9

Open Wqing35 opened 1 year ago

Wqing35 commented 1 year ago

Hi, Thanks for the great work! When I was running freePSI build according to your run_FreePSI.sh script, I encountered this problem:

截屏2023-08-07 19 49 17

Do you have any suggestions to solve this problem? Thanks a lot!

JY-Zhou commented 1 year ago

Thank you for your interest in FreePSI. I guess this error occurs due to misuse of Jellyfish. Can you show more logs on how you used Jellyfish for counting kmers and the parameter settings when calling the FreePSI build?

Wqing35 commented 1 year ago

Sorry for the late reply. Here's the script when I used Jellyfish:

截屏2023-08-17 14 28 36

It's worth to note that my input fastq amounts for 75G, that's why 10 reads.1.jf files were produced and why I set a For command to solve it. As for the error I mentioned earlier, it happened when I used FreePSI build for only one reads.1.fa produced by jellyfish dump. BTW, my K-mer is 27.

JY-Zhou commented 1 year ago

Sorry, I missed the notice about the follow-up issue. In the script you showed, I didn't see how you split the '.jf' file into 10 parts. I'm not sure if the 'jf' file can be divided into parts simply by splitting it.