alexdobin
commented
2 years ago Hi @jaichandpatel
STAR executable could not run, because some of the libraries are missing.
Please try the static executable:
--star-path /storage/apps/STAR-2.7.10a/bin/Linux_x86_64_static/
[(base) [japatel@headcoach Genome_annotation]$ rsem-prepare-reference --gtf Mus_musculus.GRCm39.107.chr.gtf --star --star-path /storage/apps/STAR-2.7.10a/bin/Linux_x86_64/ Mus_musculus.GRCm39.dna.toplevel.fa [mus_GRCm39] rsem-extract-reference-transcripts [mus_GRCm39] 0 Mus_musculus.GRCm39.107.chr.gtf None 0 Mus_musculus.GRCm39.dna.toplevel.fa Parsed 200000 lines Parsed 400000 lines Parsed 600000 lines Parsed 800000 lines Parsed 1000000 lines Parsed 1200000 lines Parsed 1400000 lines Parsed 1600000 lines Parsed 1800000 lines Parsing gtf File is done! Mus_musculus.GRCm39.dna.toplevel.fa is processed! 149419 transcripts are extracted. Extracting sequences is done! Group File is generated! Transcript Information File is generated! Chromosome List File is generated! Extracted Sequences File is generated!
rsem-preref [mus_GRCm39].transcripts.fa 1 [mus_GRCm39] Refs.makeRefs finished! Refs.saveRefs finished! [mus_GRCm39].idx.fa is generated! [mus_GRCm39].n2g.idx.fa is generated!
/storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeFastaFiles Mus_musculus.GRCm39.dna.toplevel.fa --sjdbGTFfile Mus_musculus.GRCm39.107.chr.gtf --sjdbOverhang 100 --outFileNamePrefix [mus_GRCm39] /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR: /lib64/libm.so.6: version
GLIBC_2.29' not found (required by /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR) /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.20' not found (required by /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR) /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR: /lib64/libstdc++.so.6: versionCXXABI_1.3.8' not found (required by /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR) /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.26' not found (required by /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR) /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR) "/storage/apps/STAR-2.7.10a/bin/Linux_x86_64//STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeFastaFiles Mus_musculus.GRCm39.dna.toplevel.fa --sjdbGTFfile Mus_musculus.GRCm39.107.chr.gtf --sjdbOverhang 100 --outFileNamePrefix [mus_GRCm39]" failed! Plase check if you provide correct parameters/options for the pipeline!