Hi all, I am looking to map my pair-ended trimmed reads to my reference genome using Bowtie2. I input the R1 and R2 fastq files and the reference genome FASTA file. It gives me the below error and I am not sure how to fix this.
Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 Error, fewer reads in file specified with -2 than in file specified with -1 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1Error, fewer reads in file specified with -2 than in file specified with -1
Error, fewer reads in file specified with -2 than in file specified with -1 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of ‘int’ terminate called recursively terminate called recursively (ERR): bowtie2-align died with signal 6 (ABRT)
The R1 and R2 reads are definitely same size and I also have enough space left on my galaxy for analysis. Any help much appreciated on how I can fix this please?
You may need to filter out reads shorter then 2. Do this with a tool that is made for paired-end data, cutadapt could be an option.
EDIT:
My answer may not be applicable to this problem. See: Error with bowtie2
Here the error looks slightly different.
If I quickly google " terminate called after throwing an instance of 'int'" I get a few different possible problems. Are you running bowtie2 and galaxy locally? And what steps have you done before mapping?
When I’ve seen this error, it was due to not having intact pairs present in the input fastq files.
That isn’t a requirement always but ensuring intact pairs usually solves it. There is probably a specific option that is the trigger – but I don’t know for certain which
So, if filtering by length isn’t enough (minimum seed length), try this to get rid of reads in either read dataset that no longer have a mate present in the other read dataset. In short, ensure that intact pairs are input to the tool. Some QA tools sort the outputs by paired/not state but others will just remove reads from one end.
