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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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rename in rsem-calculate-expression throws "Invalid cross-device link" #152

Open nitishnih opened 3 years ago

nitishnih commented 3 years ago

Hello,

We encountered an error with RSEM v1.3.3 running the following (paths sanitized):

rsem-calculate-expression --temporary-folder /scratch/rsemtemp --star --paired-end SRR937564_1.fastq SRR937564_2.fastq ref/mouse_ref rsem-test-star

Here /scratch is a different filesystem. The error received was:

Cannot rename /scratch/rsemtemp/rsem-test-starLog.final.out to rsem-test-star.log: Invalid cross-device link

So far, this only occurs when running rsem-calculate-expression with --star and --temporary-folder set to /scratch. I believe the problem is in this line. The issue is likely with perl's rename function given that it doesn't work across different file systems, as documented here

Let me know if I can provide more information.