Question: ectools - illegal instruction error
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gravatar for VS
17 months ago by
VS670
USA
VS670 wrote:

I'm trying to run ectools to correct PacBio reads (about 1.1Gb) for a small microbial genome. Our cluster has PBS/Torque and no SGE scheduler. So I partitioned the data into 21 directories with ~500 files each. When I run the correct.sh script, it runs and successfully creates cor.fa files in about half of the directories. In the other directories however, correct.sh script fails at the final step --

+ /home/linuxbrew/bin/python /home/software/ectoo
ls/pb_correct.py p0015 p0015.delta.snps p0015.delta.r.sc 0.96 3000 p0015

../correct.sh: line 97: 17545 Illegal instruction $python ${CORRECT_SCRIPT} ${FILE} ${FILTERED_DELTA}.snps ${FILTERED_DELTA}.r.sc ${CLR_PCT_ID} ${MIN_READ_LEN} ${FILE}

I tried to re-run the correct.sh script in these folders after removing all the intermediate delta files etc. but it fails at the same step again and again. I'm unable to wrap my head around this issue, given that the very same correct.sh script works for other folders/data partitions.

What could be going wrong here? Can anyone help me in resolving this?

Here is the command I'm giving to run the correct.sh script --

for j in {1..500}; do echo "SGE_TASK_ID=$j TMPDIR=/tmp ../correct.sh"; done | parallel -j 16
ADD COMMENTlink written 17 months ago by VS670
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