Question: error in command
0
gravatar for Bulbul Ahmed
5.0 years ago by
Bulbul Ahmed20
United States
Bulbul Ahmed20 wrote:
/trinityrnaseq/util/align_and_estimate_abundance.pl \
    --transcripts reference.fasta \
    --seqType fq \
    --left /home/file/read1.fastq \
    --right /home/file/read2.fastq \
    --est_method RSEM \
    --aln_method bowtie \
    --trinity_mode

above command i used but i found error given below (lines folded for readability)

rsem-calculate-expression --paired-end -p 4 
    --no-bam-output --bam bowtie.bam 
    /home/reference.fasta.RSEM 
    RSEM died with ret: 65280 at /trinityrnaseq/util/align_and_estimate_abundance.pl line 632

any body can find the what actually it needs?

alignment assembly • 1.9k views
ADD COMMENTlink modified 3.0 years ago by RamRS30k • written 5.0 years ago by Bulbul Ahmed20
1

Maybe its a silly comment but, are you sure that your left and right files have read1.fastq and data2.fastq names, respectively?

ADD REPLYlink written 5.0 years ago by iraun3.8k

sory its read1.fastq and read2.fastq

ADD REPLYlink written 5.0 years ago by Bulbul Ahmed20

Looks like something is missing at the end - errors usually include a line number after the "xyz.pl line" part

ADD REPLYlink written 5.0 years ago by RamRS30k

Hi, I know this was posted almost two years ago, but I have the exact same input and error! Were you ever able to figure it out?

ADD REPLYlink written 3.0 years ago by allysonm.weir0
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