Question: rsem error message: "Number of alignable reads does not match!"
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gravatar for ccshao
5.9 years ago by
ccshao10
Germany
ccshao10 wrote:

When I was running rsem (v1.2.12) on my paired-end RNA-seq data, it threw out this message: Number of alignable reads does not match!".  What could be problem? 

The running script:

rsem-calculate-expression -p 6 --paired-end fastqP_1_fa fastqP_2_fa rsemIndex EXAMPLE

and have built the reference by rsem-prepare-reference

rsem rna-seq • 2.3k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 5.9 years ago by ccshao10

What's the output of wc -l fastqP_1_fa fastqP_2_fa? My guess would be that the files are out of sync.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Devon Ryan94k

Good points. Surprisingly, when I re-run the same scripts for the same data, with only changing the number of cpu used, it works smoothly. I will submit all jobs and see the frequency of the errors.

ADD REPLYlink written 5.9 years ago by ccshao10

That's disconcerting!

ADD REPLYlink written 5.9 years ago by Devon Ryan94k

The error seems never appear again, not clear why it appears/disappears.

ADD REPLYlink written 5.9 years ago by ccshao10
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