All tests failed

[Colorstorm]

Bug

Problem

The tests for the Wochenende pipeline failed

General info

• Wochenende Version: 1.6.2
• Data: testdb/reads_R1.fastq

Command

# On console
sbatch run_Wochenende_SLURM.sh testdb/reads_R1.fastq

# In the slurm script 
python3 run_Wochenende.py --metagenome testdb --threads $cpus --testWochenende --aligner bwamem --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
python3 run_Wochenende.py --metagenome testdb --fastp --threads $cpus --testWochenende --aligner bwamem --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
python3 run_Wochenende.py --metagenome testdb --longread --threads $cpus --aligner ngmlr --readType SE --debug --force_restart $fastq
python3 run_Wochenende.py --metagenome testdb --longread --threads $cpus --aligner minimap2 --readType SE --debug --force_restart $fastq

Pipeline outpout

slurm-3145064.txt
slurm-3145075.txt
slurm-3145076.txt
slurm-3145077.txt

[colindaven]

I added the run_test.sh script recently to run the exact test needed. Please try this.

# In the slurm script 

for the first two, see if you can come up with solutions.

# running ngmlr - no tests exist for this aligner
python3 run_Wochenende.py --metagenome testdb --longread --threads $cpus --aligner ngmlr --readType SE --debug --force_restart $fastq
# running minimap2 - no tests exist for this aligner
python3 run_Wochenende.py --metagenome testdb --longread --threads $cpus --aligner minimap2 --readType SE --debug --force_restart $fastq

[colindaven]

The need for a) long reads for testing and b) using long read aligners in the test are covered here : #41