John

Few more points: 1) I was just looking at files created by bamintersect. How come there are two counts.anc_info.txt files? Can ${INTERMEDIATEDIR}/${sample_name}.counts.anc_info.txt be put in TMPDIR?

2) These files need better names: ${TMPDIR}/del_gen1 ${TMPDIR}/del_gen2 ${TMPDIR}/del_gen_reads ${TMPDIR}/filter_csv.bed3

3) Again, just pipe straight through rather than making intermediate files: a) ${TMPDIR}/geneNames.out" > "${TMPDIR}/geneNames_noBlanks.out"

b) bedmap --count "${TMPDIR}/all_regions.bed" "${TMPDIR}/filter_csv.bed3" > "${TMPDIR}/num_reads.out" paste -d $'\t' "${TMPDIR}/all_regions_and_geneNames.bed" "${TMPDIR}/num_reads.out" > "${TMPDIR}/all_regions_geneNames_numReads.bed"

I've been getting the below java errors from sort_bamintersect all morning. They are the same as the ones that were resolved with the qos adjustment before. Could this be related to the other jobs that are running on the cluster now?

There is insufficient memory for the Java Runtime Environment to continue.

Cannot create GC thread. Out of system resources.

Possible reasons:

The system is out of physical RAM or swap space

In 32 bit mode, the process size limit was hit

Possible solutions:

Reduce memory load on the system

Increase physical memory or swap space

Check if swap backing store is full

Use 64 bit Java on a 64 bit OS

Decrease Java heap size (-Xmx/-Xms)

Decrease number of Java threads

Decrease Java thread stack sizes (-Xss)

Set larger code cache with -XX:ReservedCodeCacheSize=

This output file may be truncated or incomplete.

Out of Memory Error (gcTaskThread.cpp:48), pid=140868,

tid=0x00002aaaac967700 #

JRE version: (8.0_101-b13) (build )

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.101-b13 mixed mode

linux-amd64 compressed oops)

Failed to write core dump. Core dumps have been disabled. To enable core

dumping, try "ulimit -c unlimited" before starting Java again #