search

shang-qian / SCSit

A high-efficiency cell types identification tool for single-cell sequencing data from SPLiT-seq
Other
2 stars 0 forks source link

Segmentation fault (core dumped) #3

Open LJK1991 opened 1 year ago

LJK1991 commented 1 year ago

Hello shang-qian,

I am currently trying to replicate data from this paper using SCSit. In short they perform a SPLiT-seq experiment on salt water worms. I have downloaded their data through SRAtools from their GEO Downloaded all the other required components, such as the genome and gtf files. I then replicated their read trimming with cutadapt, as mentioned in their paper for cDNA/read1: cutadapt -j 4 -m 60 -q 10 -b AGATCGGAAGAG for cellBC/read2 cutadapt -j 4 -m 94 --trim-n -q 10 -b CTGTCTCTTATA

I then concatenated all read1.fastq.gz to eachother and did the same for read2.fastq.gz creating two files. one consisting all read1 files and the second consisting of all read2 files. e.g. zcat file1.fastq.gz file2.fastq.gz file3.fastq.gz > total.fastq.gz

When running scsit i get the following error

scsit -r1 /media/draco/lucask/AlgorithmTest/ACME/data/ACME_read1.fastq.gz -r2 /media/draco/lucask/AlgorithmTest/ACME/data/ACME_read2.fastq.gz -p /media/draco/lucask/AlgorithmTest/SCSit/primerList.txt -b /media/draco/lucask/AlgorithmTest/SCSit/barcodeList.txt -t 24 -o /media/draco/lucask/AlgorithmTest/ACME/SCSit/
enter main-1enter analyzeArgs-1===>main-2 getPrimerString===>main-3 generatePrimerTable===>main-4 generateBarcTable===>main-5 generateFeatureTablestart: 763, end: 39958555521
0.00% finishing...
start: 1331, end: 39958555521
0.00% finishing...
Segmentation fault (core dumped)

I have enough disk space and RAM to run it so i dont understand why i get this error. I also don't know C++ well enough to start bug fixing. could you help me with trying to fix this error.

Thanks in advance.

oyxf commented 1 year ago

I have encoutered the same error 。The input fastq files seems should not be compressed . But when I uncompressed the files , still got the following errror: 

.....
start: 20107213, end: 37964030741
0.05% finishing...
start: 20107580, end: 37964030741
0.05% finishing...
start: 20107947, end: 37964030741
0.05% finishing...
Segmentation fault

I hope you can help us solved this running error ! Thank you very much !@shang-qian

Mayank0512 commented 1 year ago

Same error and my fastq is not compressed...also i did not get the start and end you guys are getting..all I get is segmentation fault....I am trying to run the test data the package comes with

mwLuan commented 1 year ago

@LJK1991 @oyxf @Mayank0512 ，error “Segmentation fault (core dumped)” is insufficient of your computer. Please replace better server with larger memory.

LJK1991 commented 1 year ago

@mwLuan I am very sure that is not the issue, i have sudo rights on a 256Gb RAM server. It also crashes when using the provided test data. I have also run it in different environs and by colleagues independent of telling them what the issue was. There is something else going on.

mwLuan commented 1 year ago

@LJK1991 @oyxf @Mayank0512 Sorry, in this way, we can't identify where this issue is. May you send barcode, primer and fastq data to the author's email?

jdm204 commented 7 months ago

@LJK1991 @oyxf @Mayank0512 Sorry, in this way, we can't identify where this issue is. May you send barcode, primer and fastq data to the author's email?

Hi, I can reproduce the segfault consistently with the example data in this repo: the two fastq files in test and the primer and barcode lists from data. Both the pip install version and one built from this repository segfault on the three (Linux) machines I've tested, and none were out of memory. It also doesn't seem to matter what -t is set to.

Mayank0512 commented 7 months ago

Ahhh sorry I think I sorted the issue Thanks for the help!