search

healthyPlant / PhytoPipe

10 stars 1 forks source link

Error in rule run_blastx or run_blastn #7

Open xhu556 opened 7 months ago

xhu556 commented 7 months ago

The PhytoPipe exits because of Error in rule run_blastx or run_blastn. How can I fix it?

xhu556 commented 7 months ago

This is usually caused by low quality of sequences, which results in 0 contigs. In the current version, we don't have a filter to remove bad samples. You'd better to manually remove the bad samples. Suppose you found the sample "hts_smp1" caused the problem in the log file, then you can find all "hts_smp1" related files and remove them by

runFolder=/path/my/phytopipe/run
#find files
find $runFolder -name "hts_smp1*"
#remove files
find $runFolder -name "hts_smp1*" -exec rm {} \;

Now you can rerun the pipeline without fastqDir parameter since the read files are already in the raw folder. The pipeline will continue the previous work.