Open sph17 opened 4 years ago
Sorry for the delayed response. Can you show the the precise commands you ran (starting with kevlar count
) that led to this error message? How much memory does your computer have?
Here are the scripts I ran
#!/bin/bash
#BSUB -J Kevlar_ArrayJob[6]
#BSUB -e /err_files/targz.err
#BSUB -q big
#BSUB -n 1
#BSUB mem=16G
#BSUB swp=16G
#BSUB -sla miket_sc
SOURCE_FILE_1="/kevlar/files_counttable.txt"
SOURCE_FILE_2="/kevlar/files_fastq.txt"
INPUT_1=$(sed -n ''${LSB_JOBINDEX}'p' ${SOURCE_FILE_1})
INPUT_2=$(sed -n ''${LSB_JOBINDEX}'p' ${SOURCE_FILE_2})
filename=$(basename -- "$INPUT_2")
extension="${filename##*.}"
filename="${filename%.fastq}"
OUTPUT=${filename}_novel
source activate kevlar
N_THREADS=$(nproc)
kevlar novel --out ${OUTPUT}_reads.fastq \
--control-counts /data/talkowski/sphao/projects/kevlar/YM003-C.counttable \
--case-counts ${INPUT_1} --case ${INPUT_2}
#!/bin/bash
#BSUB -J Kevlar_ArrayJob[6]
#BSUB -o /log_files/kevlarArrayJob04.log
#BSUB -e /files/err_files/targz04.err
#BSUB -q big
#BSUB -n 1
#BSUB mem=64G
#BSUB swp=64G
#BSUB -sla miket_sc
SOURCE_FILE_1="/kevlar/files_novel_reads_filtered.txt"
INPUT_1=$(sed -n ''${LSB_JOBINDEX}'p' ${SOURCE_FILE_1})
filename=$(basename -- "$INPUT_1")
extension="${filename##*.}"
filename="${filename%_novelReadsFiltered}"
OUTPUT=${filename}_partition
source activate kevlar
kevlar partition -o ${OUTPUT} ${INPUT_1}
I first ran partition at 16G as well then tried 64G
While trying the kevlar tutorial workflow, at kevlar partition step some files fail with memory error, I used 64g and 64g swap memory.