Error with alignReads.pl in Trinity?

Question

[seta]

Hi everybody,

I did transcriptome assembly using Trinity (20140717 version) and now try to run alignReads.pl using the command:

perl alignReads.pl \
  --seqType fq \
  --left all_1.fq \
  --right all_2.fq \
  --target Trinity_filtered.fasta \
  --SS_lib_type FR \
  --retain_SAM_files \
  --aligner bowtie2 \
  -- \
  -p 5

But I don't know why the following error was appeared after several minutes of running the scripts, it's:

ERROR    Error, cmd: bowtie2 -p 5 --no-head -q target left_fa > left_fa.pre.sam died with ret 256 at alignReads.pl line 763.
ERROR    Error, cmd: bowtie2 -p 5 --no-head -q target right_fa > right_fa.pre.sam died with ret 256 at alignReads.pl line 763.
Error, alignment pipeline failed due to errors encountered above. at alignReads.pl line 519.

Samtools and bowtie2 are in the PATH. Please tell me what's wrong here and how to solve it in your professional view?

Many thanks in advance,

Seta

[seta]

no suggestion, friends!