Question: ERROR:Encountered internal Bowtie 2 exception (#1) & hisat-align exited with value 1
0
gravatar for fatin nadhirah
10 months ago by
fatin nadhirah0 wrote:

I try to run and follow this tutorial https://www.bioinformatics.babraham.ac.uk/training/RNASeq_Course/Analysing%20RNA-Seq%20data%20Exercise.pdf but i got an error. Help me pls!

mfrlab:Desktop firdausraih$ hisat -x BP_index --known-splicesite-infile BP_splice_sites.txt -p 2 -U T1_1_d.fq, T1_2_d.fq, T2_1_Q30.fq, T2_2_d.fq, T5_1_d.fq, T5_2_d.fq, T6_1_d.fq, T6_2_Q30.fq | samtools view -bS - > BP_hisat.bam

-bash: samtools: command not found

Warning: Output file 'T1_2_d.fq,' was specified without -S. This will not work in future HISAT 2 versions. Please use -S instead.

Extra parameter(s) specified: "T2_1_Q30.fq,", "T2_2_d.fq,", "T5_1_d.fq,", "T5_2_d.fq,", "T6_1_d.fq,", "T6_2_Q30.fq"

Error: Encountered internal Bowtie 2 exception (#1)

Command: /Users/firdausraih/Desktop/hisat-0.1-2.6-beta/hisat-align-s --wrapper basic-0 -x BP_index --known-splicesite-infile BP_splice_sites.txt -p 2 -U T1_1_d.fq T1_2_d.fq, T2_1_Q30.fq, T2_2_d.fq, T5_1_d.fq, T5_2_d.fq, T6_1_d.fq, T6_2_Q30.fq

(ERR): hisat-align exited with value 1

rna-seq hisat • 841 views
ADD COMMENTlink modified 10 months ago by WouterDeCoster37k • written 10 months ago by fatin nadhirah0
0
gravatar for WouterDeCoster
10 months ago by
Belgium
WouterDeCoster37k wrote:

bash: samtools: command not found

This means that you have to install samtools

But it also looks like you have paired end data, for which you should use -1 and -2 rather than -U.

There is maybe also something wrong with the comma separated list with spaces.

ADD COMMENTlink written 10 months ago by WouterDeCoster37k

I've already installed samtools and export the PATH but it still says command not found. What should i do?

ADD REPLYlink written 10 months ago by fatin nadhirah0

@OP: Locate the folder where the samtools is installed. Add that folder path to your .bash_profile or .bashrc.

ADD REPLYlink modified 10 months ago • written 10 months ago by cpad011211k

i did but it still appear command not found :(

ADD REPLYlink written 10 months ago by fatin nadhirah0
1
  1. Please navigate to samtools folder where samtools executable is present and type ./samtools. If it works, then you have samtools binary
  2. Once it works, then type realpath samtools
  3. Then type echo $PATH

Output from realpath should be in path output.

ADD REPLYlink modified 10 months ago • written 10 months ago by cpad011211k

How did you install samtools?

Did you add the directory in which you installed samtools to $PATH? Check if everything is alright with

echo $PATH
ADD REPLYlink written 10 months ago by WouterDeCoster37k
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