Question: bowtie2 mapping error: core dumped
0
gravatar for lvyhwind
16 months ago by
lvyhwind0
lvyhwind0 wrote:

I am a newbie in RNA-seq analysis. When I use bowtie2 to align with paired-end fastq files, all sets of my data have a error log like this. Is there anyone knowing how to figure this out?

bowtie2 -p8 --very-sensitive --score-min=C,-15,0 --reorder --mm \
    -q -1 $reads1 -2 $reads2 -x $index \
    2> bt2_firstpass.log | samtools view -hbuS - | samtools sort - all_reads

This is the error log:

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

---when I subset a small part of paired end fastq files, everything goes well.

10000 reads; of these: 10000 (100.00%) were paired; of these:

9929 (99.29%) aligned concordantly 0 times
22 (0.22%) aligned concordantly exactly 1 time
49 (0.49%) aligned concordantly >1 times
----
9929 pairs aligned concordantly 0 times; of these:
  2387 (24.04%) aligned discordantly 1 time
----
7542 pairs aligned 0 times concordantly or discordantly; of these:
  15084 mates make up the pairs; of these:
    6131 (40.65%) aligned 0 times
    4934 (32.71%) aligned exactly 1 time
    4019 (26.64%) aligned >1 times
  

69.34% overall alignment rate

rna-seq alignment bowtie2 • 702 views
ADD COMMENTlink modified 16 months ago by genomax71k • written 16 months ago by lvyhwind0
1
gravatar for genomax
16 months ago by
genomax71k
United States
genomax71k wrote:

Error is stated in the log output.

Error, fewer reads in file specified with -2 than in file specified with -1

So your files must not have an identical number of reads and they also may be out of sync. You can use repair.sh from BBMap suite to re-sync the data and separate singletons that exist.

ADD COMMENTlink written 16 months ago by genomax71k
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