Error, fewer reads in file specified with -2 than in file specified with -1
Hai,
I'm using bowtie2 as my aliner to align my sequence. I'm getting an error Fewer reads in the file specified with -2 than in file specified with -1. i used the same file to align with BWA-mem it does not show any error. but botie2 is still running for more than 1week with the same file size.
the command i used to run bowtie2
bowtie2 -p 30 -x Reference/bowti_hg38 -1 Data/SRR622457_1.fastq -2 Data/SRR622457_2.fastq -S Output/Bowtie/Alignment/bowtie.sam
• 5,219 views
•
link
updated
by
h.mon
•
written
by
manojkumarbioinfo
•
written
by
manojkumarbioinfo
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
I need help with bowtie2 to map reads different length
written by DByter •
-
Bowtie 2 error- bowtie2-align died with signal 6 (ABRT): Help please!
written by sayema.khan •
-
alignment using bowtie2
written by adR
-
Bowtie2 alignment error with different amount of reads in R1 and R2
written by vnewtoboiin •
-
Error while using bowtie2
written by Jimpix •
-
Align reads files with diffrent number of reads using bowtie2
written by Bioinfo •
-
Bowtie2 error RNA seq aligning to genome
written by nidhi.vijayan13 •
-
Bowtie2 Alignment Error
written by chaudharyc61 •
-
Bowtie Parameter Switch Error
written by datascientist28
-
to run bowtie on multiple fastq file
written by Kritika
You need to repair the fastq files: Error with Bowtie 2
use BBMap
Did you check if there are indeed fewer sequences in one file e.g. using
wc -l? Also, one week is overly long even for a WGS sample. Probably the process died somehow and simply did not terminate properly, usetopto check if it is really running.I used BBmap repair.sh in1=r1.fq.gz in2=r2.fq.gz out1=fixed1.fq.gz out2=fixed2.fq.gz outsingle=singletons.fq.gz to fix this issue