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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Error in Prep Reference and Calculating Expression #157

Open mh425 opened 3 years ago

mh425 commented 3 years ago

Hi! I am new to RSEM so I would greatly appreciate any help I can get :)

I have been trying to run RSEM but I received the following errors:

which: no rsem-prepare-reference in (/u/local/apps/trinity/2013-08-14/gcc-4.4.7:/u/local/apps/samtools/1.9/bin:/u/local/apps/xz/5.2.3/bin:/u/local/apps/bowtie/0.12.8:/u/home/m/miniconda3/bin:/u/home/m/miniconda3/condabin:/u/local/compilers/intel/18.0.4/parallel_studio_xe_2018/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/bin/intel64:/u/local/compilers/intel/18.0.4/clck/2018.3/bin/intel64:/u/local/compilers/intel/18.0.4/itac/2018.4.025/intel64/bin:/u/local/compilers/intel/18.0.4/inspector/bin64:/u/local/compilers/intel/18.0.4/vtune_amplifier_2018/bin64:/u/local/compilers/intel/18.0.4/advisor_2018/bin64:/u/systems/UGE8.6.4/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/m/bin) ERROR, cannot find rsem-prepare-reference in PATH setting: /u/local/apps/trinity/2013-08-14/gcc-4.4.7:/u/local/apps/samtools/1.9/bin:/u/local/apps/xz/5.2.3/bin:/u/local/apps/bowtie/0.12.8:/u/home/m/miniconda3/bin:/u/home/m/miniconda3/condabin:/u/local/compilers/intel/18.0.4/parallel_studio_xe_2018/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/bin/intel64:/u/local/compilers/intel/18.0.4/clck/2018.3/bin/intel64:/u/local/compilers/intel/18.0.4/itac/2018.4.025/intel64/bin:/u/local/compilers/intel/18.0.4/inspector/bin64:/u/local/compilers/intel/18.0.4/vtune_amplifier_2018/bin64:/u/local/compilers/intel/18.0.4/advisor_2018/bin64:/u/systems/UGE8.6.4/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/m/bin

which: no rsem-calculate-expression in (/u/local/apps/trinity/2013-08-14/gcc-4.4.7:/u/local/apps/samtools/1.9/bin:/u/local/apps/xz/5.2.3/bin:/u/local/apps/bowtie/0.12.8:/u/home/m/miniconda3/bin:/u/home/m/miniconda3/condabin:/u/local/compilers/intel/18.0.4/parallel_studio_xe_2018/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/bin/intel64:/u/local/compilers/intel/18.0.4/clck/2018.3/bin/intel64:/u/local/compilers/intel/18.0.4/itac/2018.4.025/intel64/bin:/u/local/compilers/intel/18.0.4/inspector/bin64:/u/local/compilers/intel/18.0.4/vtune_amplifier_2018/bin64:/u/local/compilers/intel/18.0.4/advisor_2018/bin64:/u/systems/UGE8.6.4/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/m/bin) ERROR, cannot find rsem-calculate-expression in PATH setting: /u/local/apps/trinity/2013-08-14/gcc-4.4.7:/u/local/apps/samtools/1.9/bin:/u/local/apps/xz/5.2.3/bin:/u/local/apps/bowtie/0.12.8:/u/home/m/miniconda3/bin:/u/home/m/miniconda3/condabin:/u/local/compilers/intel/18.0.4/parallel_studio_xe_2018/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin:/u/local/compilers/intel/18.0.4/compilers_and_libraries_2018.5.274/linux/bin/intel64:/u/local/compilers/intel/18.0.4/clck/2018.3/bin/intel64:/u/local/compilers/intel/18.0.4/itac/2018.4.025/intel64/bin:/u/local/compilers/intel/18.0.4/inspector/bin64:/u/local/compilers/intel/18.0.4/vtune_amplifier_2018/bin64:/u/local/compilers/intel/18.0.4/advisor_2018/bin64:/u/systems/UGE8.6.4/bin/lx-amd64:/u/local/bin:/u/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/u/home/m/bin

Not sure what went wrong, but here is the command that I used:

/u/local/apps/trinity/2013-08-14/gcc-4.4.7/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts /u/project/trinity_out_dir/Trinity.fasta --seqType fq --left /u/project/run1.fastq --right /u/project/run2.fastq

Thank you so much!