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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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rsem-build-read-index: Please check if you provide correct parameters/options for the pipeline! #89

Open ChenMorSays opened 6 years ago

ChenMorSays commented 6 years ago

I'm getting the following errors while running rsem-calculate-expression:

rsem-parse-alignments RSEM/refs/GRCh38 rsem_temp_files/ERR841609.temp/ERR841609 rsem_temp_files/ERR841609.stat/ERR841609 star_output_1st_completed_files/ERR841609Aligned.toTranscriptome.out.bam 3 -tag XM Done!

rsem-build-read-index 32 1 0 rsem_temp_files/ERR841609.temp/ERR841609_alignable_1.fq rsem_temp_files/ERR841609.temp/ERR841609_alignable_2.fq "rsem-build-read-index 32 1 0 rsem_temp_files/ERR841609.temp/ERR841609_alignable_1.fq rsem_temp_files/ERR841609.temp/ERR841609_alignable_2.fq" failed! Plase check if you provide correct parameters/options for the pipeline!

Here's the command I'm using: RSEM/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end --append-names --calc-pme --calc-ci --num-threads 4 ? RSEM/refs/GRCh38 ?

What's going on here?

bli25wisc commented 6 years ago

Hi @PersistentlyHungry , could you provide us a minimal set of reads that can repeat this error?

ChenMorSays commented 6 years ago

Absolutely. What kind of input files would you expect? @bli25wisc