search

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
421 stars 118 forks source link

rsem-for-ebseq-calculate-clustering-info not found through conda installation #119

Open yifangt opened 5 years ago

yifangt commented 5 years ago

Hello group!

I met a problem when I run 

rsem-generate-ngvector ${REF} ${ROAD}/genome/wheat_ref
rsem-for-ebseq-calculate-clustering-info 25 /storage/yifang/20190405_RNAseq/data/rsem/genome/wheat_ref.transcripts.fa /storage/yifang/20190405_RNAseq/data/rsem/genome/wheat_ref.ump
rsem-for-ebseq-calculate-clustering-info : No such file or directory!
Please check if you have compiled the associated codes by typing related "make" commands and/or made related executables ready to use.

I tried to track the executable "rsem-for-ebseq-calculate-clustering-info", but it is NOT in my PATH or anywhere else. rsem was installed through conda:

conda install -c bioconda rsem      #version 1.3.1

What could I have missed? Thanks a lot!

cezumajo commented 4 years ago

Hi, Did you solve it? I am having trouble with this too. I am running it in a cluster and I don't seem to be able to compile 'make ebseq'!! Hence, I get the same error you got when doing rsem-generate-ngvector

I get this error:

g++ -O3 -Wall calcClusteringInfo.cpp -o rsem-for-ebseq-calculate-clustering-info /usr/bin/ld: cannot open output file rsem-for-ebseq-calculate-clustering-info: Permission denied collect2: error: ld returned 1 exit status make[1]: [rsem-for-ebseq-calculate-clustering-info] Error 1 make[1]: Leaving directory `/geode2/soft/hps/rhel7/rsem/gnu/1.3.0/EBSeq' make: [ebseq] Error 2

Amar343 commented 2 years ago

I'm also getting same error after run following command Software/RSEM-1.3.3/rsem-generate-ngvector /home/amar/Downloads/RSEM_MASTER/NewData/Ref_index/Zea_mays.transcripts.fa trans_ref rsem-for-ebseq-calculate-clustering-info 25 /home/amar/Downloads/RSEM_MASTER/NewData/Ref_index/Zea_mays.transcripts.fa trans_ref.ump rsem-for-ebseq-calculate-clustering-info : No such file or directory! Please check if you have compiled the associated codes by typing related "make" commands and/or made related executables ready to use. please help me, my system properties 7.6 GiB memory, Intel® Core™ i5-8500 CPU @ 3.00GHz × 6 processor, 1 TB disk capacity

mrubio-chavarria commented 2 years ago

Hi, For me, within the RSEM folder:

cd EBSeq
make install

That worked for me. The script appeared in the EBSeq folder and rsem-generate-ngvector recognised it.

HarveyWWW commented 8 months ago

Hello, groups！ I met the same problem today, and for me: cd RSEM/EBSeq/ make rsem-for-ebseq-calculate-clustering-info Then it worked.

The following reply is: wuzeyu@luo-lab-tower:~/data_wzy/wuzeyu/software/RSEM-1.3.1/EBSeq$ /home/wuzeyu/data_wzy/wuzeyu/software/RSEM-1.3.1/rsem-generate-ngvector /home/wuzeyu/data_wzy/wuzeyu/transcripts_quant/reference/genome/hg38/GRCh38.p14.genome.fa human_p14 rsem-for-ebseq-calculate-clustering-info 25 /home/wuzeyu/data_wzy/wuzeyu/transcripts_quant/reference/genome/hg38/GRCh38.p14.genome.fa human_p14.ump rsem-for-ebseq-calculate-clustering-info : No such file or directory! Please check if you have compiled the associated codes by typing related "make" commands and/or made related executables ready to use. wuzeyu@luo-lab-tower:~/data_wzy/wuzeyu/software/RSEM-1.3.1/EBSeq$ make rsem-for-ebseq-calculate-clustering-info g++ -O3 -Wall calcClusteringInfo.cpp -o rsem-for-ebseq-calculate-clustering-info wuzeyu@luo-lab-tower:~/data_wzy/wuzeyu/software/RSEM-1.3.1/EBSeq$ /home/wuzeyu/data_wzy/wuzeyu/software/RSEM-1.3.1/rsem-generate-ngvector /home/wuzeyu/data_wzy/wuzeyu/transcripts_quant/reference/genome/hg38/GRCh38.p14.genome.fa human_p14 rsem-for-ebseq-calculate-clustering-info 25 /home/wuzeyu/data_wzy/wuzeyu/transcripts_quant/reference/genome/hg38/GRCh38.p14.genome.fa human_p14.ump The reference is loaded. All possbile 25 mers are generated.