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genome-vendor / bsmap

Unofficial repo for software vendoring or packaging purposes
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buffer overflow detected ***: #7

Open CS791 opened 4 years ago

CS791 commented 4 years ago

Hi! I am trying to BSMAP using following command line:

"bsmap-2.90/bsmap -a /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R1_val_1.fq.gz -b /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R2_val_2.fq.gz -d /media/waqas/Chaudhary/Bsmap_Output/Ath_ChrAll.fa -o /media/waqas/Chaudhary/Bsmap_Output/DataA/epiRIL-368_Rep1_L1.bam -p 6"

The error pop in as: "[bsmap] @Sat Apr 11 17:52:04 2020 loading reference file: /media/waqas/Chaudhary/Bsmap_Output/Ath_ChrAll.fa (format: FASTA) [bsmap] @Sat Apr 11 17:52:05 2020 7 reference seqs loaded, total size 119667750 bp. 1 secs passed [bsmap] @Sat Apr 11 17:52:08 2020 create seed table. 4 secs passed [bsmap] @Sat Apr 11 17:52:08 2020 Pair-end alignment(6 threads), Input read file #1: /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R1_val_1.fq.gz (format: gzipped FASTQ) Input read file #2: /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R2_val_2.fq.gz (format: gzipped FASTQ) Output file: /media/waqas/Chaudhary/Bsmap_Output/DataA/epiRIL-368_Rep1_L1.bam buffer overflow detected : bsmap-2.90/bsmap terminated Aborted (core dumped)"

I need help to troubleshoot this error. Any help is much appreciated.

Thanks

SC

chrisamiller commented 4 years ago

This repository is a fork of the main bsmap project for convenience. We didn't write it and no longer use it, so unfortunately can't be much help.