Question: rsem error message: "Number of alignable reads does not match!"
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ccshao • 10 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
What's the output of
wc -l fastqP_1_fa fastqP_2_fa? My guess would be that the files are out of sync.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.
That's disconcerting!
The error seems never appear again, not clear why it appears/disappears.