rsem-calculate-expression error

[komalsrathi]

Hello,

I am trying to quantify results from STAR but I am getting error using the rsem-calculate-expression command:

This is with version: RSEM v1.2.31

$ rsem-calculate-expression --version
Current version: RSEM v1.2.31

RSEM Reference:

$ ls rsem_ref_hg38
gencode.v23.annotation.gtf  hg38.chrlist  hg38.fa  hg38.grp  hg38.idx.fa  hg38.n2g.idx.fa  hg38.seq  hg38.ti  hg38.transcripts.fa

STAR command:

$ /mnt/isilon/cbmi/variome/bin/star/STAR-2.5.2b/bin/Linux_x86_64/STAR --runThreadN 4 --limitBAMsortRAM 33874361894 --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38 --outFileNamePrefix rna --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz --readFilesCommand zcat

This generated the following bam files:

rnaAligned.sortedByCoord.out.bam
rnaAligned.toTranscriptome.out.bam

RSEM command:

$ rsem-calculate-expression --paired-end --no-bam-output --quiet --no-qualities -p 4 --forward-prob 0.5 --seed-length 25 --fragment-length-mean -1.0 --bam rnaAligned.toTranscriptome.out.bam /mnt/isilon/cbmi/variome/reference/rsem_hg38/hg38 rna

rsem-parse-alignments /mnt/isilon/cbmi/variome/reference/rsem_hg38/hg38 rna.temp/rna rna.stat/rna rnaAligned.toTranscriptome.out.bam 2 -tag XM -q

rsem-build-read-index 32 0 1 rna.temp/rna_alignable_1.fa rna.temp/rna_alignable_2.fa

rsem-run-em /mnt/isilon/cbmi/variome/reference/rsem_hg38/hg38 2 rna rna.temp/rna rna.stat/rna -p 4 -q
rsem-run-em: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by rsem-run-em)
"rsem-run-em /mnt/isilon/cbmi/variome/reference/rsem_hg38/hg38 2 rna rna.temp/rna rna.stat/rna -p 4 -q" failed! Plase check if you provide correct parameters/options for the pipeline!

What am I doing wrong here?

[bli25wisc]

Hi @komalsrathi,

First, can you try 'make clean' and 'make' to recompile RSEM from source and see if you are out of this problem? If it does not help, you can follow these links:

http://stackoverflow.com/questions/5216399/usr-lib-libstdc-so-6-version-glibcxx-3-4-15-not-found

http://stackoverflow.com/questions/31525271/usr-lib64-libstdc-so-6-version-glibcxx-3-4-15-not-found

Best, Bo

[komalsrathi]

There may have been compiling problems but I just used the conda version and it works.