Comments (4)
Can you paste here the command you used to launch SparkBWA?
from sparkbwa.
Here (same works with paired reads)
spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose
$EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r --hdfs --index $ {Index_File} -n 100 data/R1.fastq data/Output_ERR000589_sam
For completeness - paired-reads command:
spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose
$EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r -p --hdfs --index $ {Index_File} -n 100 data/R1.fastq data/R2.fastq data/Output_ERR000589_sam
from sparkbwa.
SparkBWA, by default, uses paired reads. To use single reads you need to specify the "-s" option. It should be something like:
spark-submit --conf spark.ui.enabled=true --class com.github.sparkbwa.SparkBWA --master yarn --deploy-mode cluster --driver-memory 40G --executor-memory 20G --executor-cores 4 --num-executors 100 --verbose
$EBROOTSPARKBWA/SparkBWA-0.2.jar -m -r -s --hdfs --index $ {Index_File} -n 100 data/R1.fastq data/Output_ERR000589_sam
I am going to update the documentation with all the available options. Please, let me know if this works for you.
from sparkbwa.
Thank you. With explicitly putting '-s' it works. I had the feeling I had done it before but maybe it was not on HDFS data.
edit: works on Spark standalone too. Thanks.
from sparkbwa.
Related Issues (20)
- mvn package compilation failing with certificate error HOT 3
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- Index file cannot be located HOT 1
- Error when using Azure blob storage paths for FASTQ files and SAM output file HOT 1
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from sparkbwa.