ERROR:Encountered internal Bowtie 2 exception (#1) & hisat-align exited with value 1

Question

[fatin nadhirah]

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

Answer 1

[WouterDeCoster]

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.

[fatin nadhirah]

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

[cpad0112]

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

[fatin nadhirah]

i did but it still appear command not found :(

[cpad0112]

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.

[WouterDeCoster]

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