nmquijada/tormes

Run stopped

Opened this issue · 2 comments

ddesai5 commented

Hello, I am running tormes for the first time on a mac. This is the 'error' I am getting. Thanks!

Warning message:
In read.table("ecoli_practice/output_genomes/ERR022075metadata.txt", :
incomplete final line found by readTableHeader on 'ecoli_practice/output_genomes/ERR022075metadata.txt'

  • All the software is properly installed.
  • The data included in the metadata file is correct.

tormes version 1.3.0 analysis will start now

Status can be seen in "/Users/abc/sequence_analysis/ERR022075_1/tormes.log"

/Users/abc/opt/anaconda3/envs/tormes-1.3.0/bin/tormes: line 929: syntax error near unexpected token >' /Users/abc/opt/anaconda3/envs/tormes-1.3.0/bin/tormes: line 929: if ls $OUTWD/Raw_reads/*fastq &>>/dev/null; then'

biobrad commented

Hi @ddesai5
Did you create your metadata file in windows or in linux?
Check that the file is unix compatible for 'new line'. If you are using windows, use notepad++ and make sure that under the edit menu that EOL Conversion is set to Unix.

Alternatively, you can put your fasta files and .fastq.gz files in a folder, then run this script which will create the samples_metadata.txt file for you with all the correct spacing etc:

https://github.com/biobrad/Tormes-Meta-Create/blob/main/tormes_meta_create

good luck.
cheers
Brad

nmquijada commented

Hi @ddesai5
Did you try @biobrad solution?

Alternatively, you can run TORMES again but by redirecting the output:

[YOUR TORMES COMMAND] &>>error-tormes.txt 2>>error-tormes.txt &

By doing so, you won't see anything in the terminal. This is intended, so please don't kill the process. The command will record everything occurring in your tormes run, errors included, so we might be able to track them.
Once the analysis is done, please share with us the error-tormes.txt file

Thanks,
Narciso