Entering edit mode
5.5 years ago
Mostafa Mahmoud
•
0
hi, I have 60 samples 10g of RNA seq I using Trinity to do denovo assembly but i can't figure out resource usage i am running using qsub to submit it main node every time job canceled i don't know why the server have 2tb memory.
You may want to check this with your cluster admin, Possibly other jobs may be running. Or try with some small demo file first before running your actual data.
I Tryed one sample is ok.
Post qsub script and error messages.
i just export my PATH apps and simply add the command in file then qsub denovo.sh
cat denovo.sh
export PATH=/bin:/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/bin:/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/public/home/jmwu/.linuxbrew/bin:/public/home/jmwu/.linuxbrew/sbin:/public/home/jmwu/miniconda/bin:/public/home/jmwu/00.soft/exonerate-2.2.0-x86_64/bin:/public/home/jmwu/cxpeng/FastQC:/public/home/jmwu/00.soft/EVidenceModeler-1.1.1/EvmUtils:/public/home/jmwu/00.soft/genBlast_v138_linux_x86_64:/public/home/jmwu/00.soft/LightAssembler:/public/home/jmwu/00.soft/last.soft/bin:/public/home/jmwu/00.soft/miniasm:/public/home/jmwu/00.soft/minimap:/public/home/jmwu/00.soft/jdk1.8.0_111/bin:/public/home/jmwu/00.soft/shapeit/bin:/public/home/jmwu/00.soft/vcftools/vcftools_0.1.13/bin:/public/home/jmwu/00.soft/canu/Linux-amd64/bin:/public/home/jmwu/00.soft/DBG2OLC:/public/home/jmwu/00.soft/DBG2OLC/utility:/public/home/jmwu/00.soft/DBG2OLC/compiled:/public/home/jmwu/00.soft/AssemblyUtility/compiled:/public/home/jmwu/00.soft/bbmap:/public/home/jmwu/00.soft/PBSuite_15.8.24/pbsuite/jelly:/public/home/jmwu/00.soft/PBSuite_15.8.24/bin:/public/home/jmwu/00.soft/Python-2.7.soft/bin:/public/home/jmwu/00.soft/proovread/util/SeqFilter/bin:/public/home/jmwu/00.soft/proovread/util/SeqFilter/bin:/public/home/jmwu/00.soft/proovread/util/shrimp-2.2.3:/public/home/jmwu/00.soft/proovread/util/blasr-1.3.1:/public/home/jmwu/00.soft/blasr/hdf5/hdf5-1.8.16-linux-centos6-x86_64-gcc447-shared/bin:/public/home/jmwu/00.soft/DAZZ_DB:/public/home/jmwu/00.soft/DALIGNER:/public/home/jmwu/00.soft/proovread/bin:/public/home/jmwu/00.soft/StriDe.soft/bin:/public/home/jmwu/00.soft/sparsehash.soft:/public/home/jmwu/00.soft/ActivePerl-5.18/bin:/public/home/jmwu/00.soft/bin:/public/home/jmwu/00.soft/cmake.soft/bin:/public/home/jmwu/00.soft/Platanus_v1.2.4:/public/home/jmwu/00.soft/FGAP/FGAP_1_8_1_LINUX64b:/public/home/jmwu/00.soft/FGAP/FGAP_1_8_1_LINUX64b/blast:/public/home/jmwu/00.soft/bin/blast:/public/home/jmwu/00.soft/FGAP/MCR/v717/bin:/public/home/jmwu/00.soft/hdf5/bin:/public/home/jmwu/00.soft/DEXTRACTOR:/public/home/jmwu/00.soft/MECAT/Linux-amd64/bin:/usr/lib64/qt-3.3/bin:/public/software/mpi/openmpi/1.6.5/intel/bin:/opt/gridview//pbs/dispatcher-sched/bin:/opt/gridview//pbs/dispatcher-sched/sbin:/opt/gridview//pbs/dispatcher/bin/lsf_cmd:/opt/gridview//pbs/dispatcher/bin:/opt/gridview//pbs/dispatcher/sbin:/public/software/compiler/intel/composer_xe_2013_sp1.0.080/bin/intel64:/opt/gridview//clusconf/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:::::::/public/home/jmwu/00.soft/PBSuite_15.8.24//bin/:/public/home/jmwu/00.sddoft/busco:/public/home/jmwu/00.soft/sortmerna-2.1b:/public/home/jmwu/bin:/public/home/jmwu/00.soft/sratoolkit.2.4.1-ubuntu64/bin:/public/home/jmwu/bin:/public/home/jmwu/miniconda/jre/bin:$PATH export JAVA_HOME=/public/home/jmwu/miniconda/jre/bin/java
Trinity --samples_file /public/home/jmwu/rna/diet/sample --trimmomatic --seqType fq --max_memory 1000G --CPU 50 --output /public/home/jmwu/rna/diet/trinity_out_dir/
i dont know how to write qsub script !!!!
The default queue probably has low memory limit, and you may be exceeding this limit. Contact your sysadmins for instructions on how to 1) use the queuing system in general; 2) use the large memory queue; and 3) write qsub scripts.