ARRIBA persistent failure

[slsevilla]

Problem:

• Xinyu is getting a persistent error with a subset of samples related to rule ARRIBA

Example log info:

cat /data/khanlab2/processed_DATA/ngs_pipeline_SJ031111=SJEPD031111_D1=20220911_20221116_151637.log | grep "arriba"

/data/khanlab2/processed_DATA/log/arriba.52717235.e

Relevant error code:

cp: cannot create regular file ‘/data/khanlab2/processed_DATA//SJ031111/SJEPD031111_D1/SJEPD031111_D1_T_H2HL5BBXY/fusion/arriba-fusion.txt’: No such file or directory

In reviewing this file, I can see that this does exist. This means that the second attempt of this rule completed, as expected.

for f in /data/khanlab2/processed_DATA/log/arriba.527*.e; do flag=`cat $f | grep "SJEPD031111_D1_T_H2HL5BBXY"`; if [[ $flag != "" ]]; then echo $f; fi; done
/data/khanlab2/processed_DATA/log/arriba.52717235.e
/data/khanlab2/processed_DATA/log/arriba.52755354.e

Solution:

• This seems to be sporadic and much less consistent amongst all samples. For now I'm going to close this as it does appear to resolve itself. Hopefully the solutions implemented in issue #15 and #16 will help to either clear this issue or elucidate what is going on with these failures.