rsem-generate-ngvector( 1.3.0) failed

[wangyugui]

Hi.

rsem-generate-ngvector( 1.3.0) failed with the flowing message.

# rsem-generate-ngvector ./rna.fa rsem
rsem-for-ebseq-calculate-clustering-info 25 ./rna.fa rsem.ump
The reference is loaded.
All possbile 25 mers are generated.
All 25 mers are sorted.
Clustering information is calculated.

rsem-for-ebseq-generate-ngvector-from-clustering-info rsem.ump rsem.ngvec
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  line 29593 did not have 2 elements
Calls: read.table -> scan
Execution halted
"rsem-for-ebseq-generate-ngvector-from-clustering-info rsem.ump rsem.ngvec" failed! Plase check if you provide correct parameters/options for the pipeline!
[root@T620 GRCh38.p10]# rsem-for-ebseq-generate-ngvector-from-clustering-info
Usage: rsem-for-ebseq-generate-ngvector-from-clustering-info input_file output_file

#

the line 29593 of rsem.ump  is :
NM_007285.6 Homo sapiens GABA type A receptor associated protein like 2 (GABARAPL2), mRNA       0.0129096

[wangyugui]

By the way, 'make prefix=/usr/hpc-bio/RSEM-1.3.0 -j 24 install' does NOT install rsem-generate-ngvector. I have to copy them by myself.

[wangyugui]

When I convert the rna.fa file by 'awk '{if(NF>=2){print $1}else{print $0}}' rna.fa >rna2.fa', then 'rsem-generate-ngvector ./rna2.fa rsem' works.

so there should be a problem when parsing fasta file.