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UCSC-LoweLab / tRNAscan-SE

A program for detection of tRNA genes
GNU General Public License v3.0
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Unable to open /tmp/tscan16133_cm_SeC.out for reading. Aborting program. #4

Closed yqchen17 closed 3 years ago

yqchen17 commented 3 years ago

Hi, I just installed tRNAscan-SE today, but when it outputted to around line 2500, it suddenly stopped and got an error. (Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan Unable to open /tmp/tscan16133_cm_SeC.out for reading. Aborting program.)

The first time I got an error like the bug here https://github.com/UCSC-LoweLab/tRNAscan-SE/issues/2, which was kind of a bug related to isotype-specific search.

The second time I added the parameter '-S off' as recommended, however I still got the error at nearly the same output line.

Could anyone help me out here?

yqchen17 commented 3 years ago

I have figured it out. For a large fasta file, you should split it into several pieces (in my case around 2000 fasta files for one time). I don't need to swith -S off and it runned smoothly.