"Floating point exception" when using bowtie

Question

[szp770]

Hi ,all. When I try to use bowtie to remove rRNA from the data, it showed error 'work.sh: line 1: 22592 Floating point exception(core dumped)'. My command is:

bowtie -v 2 -l 18 -p 4 GRCh37.p13_rRNA_index Stau1.trimA.fq --un Stau1.nonrRNA.fq > /dev/null 2> Stau1.map_to_rRNA_read.log

Actually it showed up 'nonrRNA.fq' file(but within a few seconds), and the 'log' file is empty. How to deal with this trouble. Thanks!

[GenoMax]

Do you have any reads that are empty i.e. have no sequence in Stau1.trimA.fq? What trimming program did you use?

[szp770]

the fq file is not empty. however, the fq file has two repeats, one is about 700M, another is 1.8G. I use "trim_galore -q 25 --phred33 -e 0.1 --length 36 --stringency 3" to trim raw data, but fastqc result is not very good.

[GenoMax]

I was not referring to fq file being empty but a fastq record. You may have one (or more) records where the entire sequence may have been removed by trim_galore leaving just an empty fastq header behind.

[szp770]

the Stau1.trimA.fq file is not empty after treating with trim_galore. It has 21881384 lines counting by "wc -l"

[ATpoint]

Is this being run from a script (work.sh)? If so please run it on a representative sample from command line, only the bowtie command. Syntax should be correct afai can see, but 'work.sh: line 1: 22592 Floating point exception(core dumped)' indicates a scripting error. If you need help debugging then please add the script.

[szp770]

yes, I print the shell command in a sh filework.sh), the commands are as follows:

bowtie -v 2 -l 18 -p 4 GRCh37.p13_rRNA_index Stau1-1.trimA.fq --un Stau1-1.nonrRNA.fq 1> /dev/null 2> Stau1-1.map_to_rRNA_read.log
bowtie -v 2 -l 18 -p 4 GRCh37.p13_rRNA_index Stau1-2.trimA.fq --un Stau1-2.nonrRNA.fq 1> /dev/null 2> Stau1-2.map_to_rRNA_read.log

then I use nohup bash work.sh & to run the command, within a few seconds, the nonrRNA.fq came out, but log file is empty. and when "less nohup.out", it showed 'work.sh: line 1: 22592 Floating point exception(core dumped)'