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Error with bowtie2

Hi,

I encounter a error when I am running the bowtie2 for genome mapping.

I use the latest version, which is bowtie2. 2.3

After installing bowtie2, I build the index for it, which run successfully and the index files are generated. Then I began to mapping using the following command:

bowtie2 \
  -N 1 \
  -x Atbt2index \
  -1 /home/zxu/document/GATA_ChIP-seq/CGA1_INPUT_Rep1_R1.fastq \
  -2 /home/zxu/document/GATA_ChIP-seq/CGA1_INPUT_Rep1_R2.fastq \
  --un /home/zxu/document/GATA_ChIP-seq/Unaligned_CGA1_INPUT_Rep1.fq \
  -S /home/zxu/document/GATA_ChIP-seq/CGA1_INPUT_Rep1.sam

At the beginning the program run successfully, and I can see the both the sam file and the file for unaligned read are generated. And I can also see the file size of .sam is increasing as the program running. However, when the file size increased around 1GB, the program died with the following information.

Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of 'int'
bowtie2-align died with signal 6 (ABRT) (core dumped)

The sam file can still be opened and I can see the data in there, I assume that the data is not complete. And the file for the unaligned reads are still empty with noting in it.

It seems like it is the problem of my input files. Anyone knows what is going on with my file data? Many thanks.

Zhenhua

bowtie2
• 6,520 views • link
updated by Ram Ram • written by zhhxu9 • zhhxu9

What's the output of wc -l /home/zxu/document/GATA_ChIP-seq/CGA1_INPUT_Rep1_R?.fastq?

• 1 views • link
written by Devon Ryan Devon Ryan

I am getting the same problem... while using Trinity though...

output of `wc -l`

127349656 /home/kaalindi/3N/3Nleft.fastq

• 0 views • link
written by kanika.151 kanika.151

Presumably the other file has more/fewer reads. You should find out why that happened and fix it.

• 0 views • link
written by Devon Ryan Devon Ryan

I believe you have files with different numbers of reads. You should check this and verify the existence of singletons.

• 0 views • link
written by RafaelMP RafaelMP

1 answer

I am getting the same problem and the read size is exactly same for both files. The command aborted after generating more than 55GB of sam. Now, I am afraid this doesnt represent the whole data

Can anybody help me in that?

• 0 views • link
written by micro32uvas • micro32uvas

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