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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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EukHighConfidenceFilter fails to write output file #8

Closed sanaek closed 3 years ago

sanaek commented 3 years ago

Hello, I'm running EukHighConfidenceFilter to trnaScan-SE detail output but fails to write its output (either on my personal computer and on cluster server). The command I used is the following:

EukHighConfidenceFilter -i forficula.consensus.v1sta.masked.out -s trna.strc.for.tbl -p euk.conf.for -o /eukconfi

and the final message of the program:

Status: Writing output file /eukconfi/euk.conf.for.out Fail to open /eukconfi/euk.conf.for.out

Is this related to writing permissions? Im sorry if this is too basic, Im new to bioinformatics.

Thank you

patriciaplchan commented 3 years ago

Please check if the output directory /eukconfi is already existed. If not, you will have to create it before running the tool.

sanaek commented 3 years ago

I created the folder before running EukHighConfidenceFilter and the error is the one above, I tried not creating it also, but the issue is the same

patriciaplchan commented 3 years ago

Do you receive other error messages before the one you listed? Can you send all the output messages when running the tool?

sanaek commented 3 years ago

Hello

EukHighConfidenceFilter -i forficula.consensus.v1sta.masked.out -s trna.strc.for.tbl -p euk.conf.for -o /eukconfi mkdir: /eukconfi: Read-only file system Status: Filtering pseudogenes Use of uninitialized value $header{"hmm_score"} in array element at /Users/sanae/anaconda3/envs/trna/bin/EukHighConfidenceFilter line 381, <FILE_IN> line 7. ..... Argument "scaffold_36448" isn't numeric in numeric lt (<) at /Users/sanae/anaconda3/envs/trna/bin/EukHighConfidenceFilter line 457. Status: Tertiary filtering Status: Writing output file /eukconfi/euk.conf.for.out Fail to open /eukconfi/euk.conf.for.out

Thats about it (... indicate the other lines running)

Thank you!

patriciaplchan commented 3 years ago

It looks like you have two problems. 1) You have a read-only file system error when creating directory /eukconfi. This means that you have no access right to create the directory. You will have to change access permission or use another output directory. 2) The tool was not able to find the hmm_score column in the tRNAscan-SE output file. When running tRNAscan-SE, please make sure to include "-H --detail" as options. If you did not do that, please run it again before running EukHighConfidenceFilter.

sanaek commented 3 years ago

Great, thank you for you help!