Rsem-calculate-expression doesn't report reads processed and other stats
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7.5 years ago
AW ▴ 350

Hi,

I'd be very grateful for any comments on my question.

I previously ran the following Rsem command on multiple paired end samples and got the following output:

rsem-calculate-expression -p 12 --bowtie-chunkmbs 2048 --paired-end forward reverse Trinity_ref
[samopen] SAM header is present: 102479 sequences.
# reads processed: 383736373
# reads with at least one reported alignment: 362860697 (94.56%)
# reads that failed to align: 20875676 (5.44%)
Reported 446379144 paired-end alignments to 1 output stream(s)
[bam_sort_core] merging from 360 files...

However, I ran the following command and got the following output:

rsem-calculate-expression -p 12 --bowtie-chunkmbs 2048 --paired-end forward reverse different_Trinity_ref
[samopen] SAM header is present: 78359 sequences.
[bam_sort_core] merging from 24 files...

Why has the second run not generated the stats output that the first did? There were no errors and the run completed and produced the genes.results and isoforms.results.

Thanks

Alison

RSEM RNA-Seq • 3.0k views
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