Error while running HISAT2

0

Entering edit mode

7.6 years ago

rob.costa1234 ▴ 310

I have paired end RNAseq data that has been trimmed individual AFSTq file, when I ran hisat2 it gives me following error-

Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

Any one can advice what may be wrong I tried to google it but no hit came.

Thanks

Rob

RNA-Seq • 4.6k views

ADD COMMENT • link 7.6 years ago by rob.costa1234 ▴ 310

2

Entering edit mode

How did you trim the fastq files? Did you trim each file of the pair separately? Because if you did, you shouldn't.

ADD REPLY • link 7.6 years ago by h.mon 35k

2

Entering edit mode

The error means that you don't have the same number of reads in the forward as in the reverse file.

ADD REPLY • link 7.6 years ago by WouterDeCoster 48k

1

Entering edit mode

You could repair.sh the data using BBMap suite or as @h.mon indicated, ideally go back and re-do the trimming with R1/R2 together.

ADD REPLY • link 7.6 years ago by GenoMax 154k

Login before adding your answer.