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msuite's Issues

Segmentation Fault and pipeline crash with bowtie2.processer.pe

Hi

Ive been trying to run Msuite now a few times and each time i get to the step where the bowtie2.processer.pe step runs, it crashes with a segmentation fault.. Below is what shows in the terminal..

INFO: 1 paired fastq files will be loaded.
Done: 134567031 lines processed.
...python3_msuite/bin/bowtie2 -q --ignore-quals --no-unal -p 38 --sam-no-qname-trunc -x .../msuite/index/hg38/Mode3/C2T --dovetail --minins 0 --maxins 1000 -1 Msuite.R1.fq -2 Msuite.R2.fq -S Msuite.C2T.sam 2>Msuite.C2T.log
...python3_msuite/bin/bowtie2 -q --ignore-quals --no-unal -p 38 --sam-no-qname-trunc -x .../msuite/index/hg38/Mode3/G2A --dovetail --minins 0 --maxins 1000 -1 Msuite.R1.fq -2 Msuite.R2.fq -S Msuite.G2A.sam 2>Msuite.G2A.log
.../msuite/bin/bowtie2.processer.pe Msuite.C2T.sam Msuite.G2A.sam Msuite.trim.log Msuite.merged.sam 8 >Msuite.merge.log
Segmentation fault
makefile:12: recipe for target 'Msuite.merge.log' failed
make: *** [Msuite.merge.log] Error 139

Any ideas/suggestions whats causing the crash?
For note though, i do change the bowtie 2 running command to

...python3_msuite/bin/bowtie2 -q --ignore-quals --no-unal -p 38 --sam-no-qname-trunc -x .../msuite/index/hg38/Mode3/C2T --dovetail --minins 0 --maxins 1000 -1 Msuite.R1.fq -2 Msuite.R2.fq -S Msuite.C2T.sam 2>Msuite.C2T.log

missing KSLIB::Koverlap

Hello hello!

I'd like have a go of your modified Sherman, can you share the KSLIB::Koverlap module involved?

Cheers,
Richard

Issue with genome index build

Hey team,

I am not sure, if the tool has been optimized for ensembl genome annotations.

I did some formatting and prefixing with "chr" on individual chr<#>.fa.gz and the annotation.gtf.gz file.

#code
bash /N/project/Sen_Lab_Omics/RAJNEESH/Software/Msuite/build.index/build.index.sh -h
Usage: /N/project/Sen_Lab_Omics/RAJNEESH/Software/Msuite/build.index/build.index.sh <genome folder|fa> <refSeq.txt> <index.identifier> [thread=auto]

This is a utility program of Msuite, designed to build genome references.
Please refer to README file for more information.

#build index
bash /path/Msuite/build.index/build.index.sh /path/msuite_index/Genome_Dir/ /path/msuite_index/hg38_genes.txt.gz hg38
=> INFO: Threads used: 24

Except for thread information, I am getting no output.

Any suggestion or pseudo code would be highly appreciated!

  • Raj

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