rsem error message: "Number of alignable reads does not match!"

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7.7 years ago

ccshao ▴ 10

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 • 3.1k views

ADD COMMENT • link updated 4 months ago by Ram 35k • written 7.7 years ago by ccshao ▴ 10

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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 REPLY • link 7.7 years ago by Devon Ryan 101k

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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 REPLY • link 7.7 years ago by ccshao ▴ 10

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That's disconcerting!

ADD REPLY • link 7.7 years ago by Devon Ryan 101k

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

ADD REPLY • link 7.7 years ago by ccshao ▴ 10

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