Troubleshooting

Introduction

This page provides the common errors and solutions for jobs at GACRC cluster. The examples are made from Sapelo2 environment, but the solutions apply to Linux clusters as well.

File format

The text files, such as submission script, fasta file or other text data files at Linux should be in ASCII format. If the files are generated under other operating system or copied from the web, there could introduce hidden characters which cannot be recognized by Linux. Hence bring the error for the job. There are many posts elaborating on this problem, such as editpadpro

Here is the command to check on the file format, using file sub.sh as an example file name below:

file sub.sh

The expected the correct format is ASCII. There could be a variation of response, such as python script, ASCII with long lines. All these responses are acceptable as long as it is ASCII text format without wrong endings:

sub.sh: Bourne-Again shell script, ASCII text

Here are common wrong formats:

sub.sh: Bourne-Again shell script, UTF-8 Unicode text executable
sub.sh: Bourne-Again shell script,  ASCII text, with CRLF line terminators

Most time it is easy to be fixed by saving the file in Unix format or using the following command at cluster:

dos2unix sub.sh

For the file in UTF-8 Unicode encoding, the easiest way is to manually remove the weird characters in a Linux text editor, such as vi, nano or pico.

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Invalid DISPLAY variable

Python script using matplotlib complains DISPLAY error. It is observed in faststructure, oligotyping, QIIME and other applications. Such as in QIIME:

ml qiime/1.9.1_conda
conda activate /usr/local/apps/gb/qiime/1.9.1_conda
python /usr/local/apps/gb/qiime/1.9.1_conda/bin/core_diversity_analyses.py 
...
File "/usr/local/apps/gb/qiime/1.9.1_conda/lib/python2.7/site-packages/matplotlib/backends/backend_qt5.py", line 138, in _create_qApp
    raise RuntimeError('Invalid DISPLAY variable')
RuntimeError: Invalid DISPLAY variable

The solution is to define DISPLAY backend before the function script:

ml qiime/1.9.1_conda
conda activate /usr/local/apps/gb/qiime/1.9.1_conda
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
python /usr/local/apps/gb/qiime/1.9.1_conda/bin/core_diversity_analyses.py

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Unrecognized lines following backslash line continuation

In case of using backslash to continue the lines, there should be no extra space after backslash. Otherwise the following lines will be parsed as separate command and cause errors:

#PBS -S /bin/bash
#PBS -N j_blast
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=8:00:00
#PBS -l mem=10gb
#PBS -M username@uga.edu
#PBS -m abe

cd $PBS_O_WORKDIR

module load BLAST+/2.7.1-foss-2016b-Python-2.7.14
blastn -num_threads 4 \
-db /db/ncbiblast/nrte/latest/nt \ 
-query my_fasta.fa

There is a space at line "-db /db/ncbiblast/nrte/latest/nt \ ". This will cause error as "-query my_fasta.fa" being taken as an individual command. The blast command will throw error as "Error: Too many positional arguments ..." since there is no input file found.

The solution is to remove the extra space.

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