Hisat2 Error

Question

[Laila]

Hi everyone! I am now working on the wheat genome (Triticum aestivum) with 14.8Gb. Because I am working on my personal device, I tried to download the first chromosome (A1) to work with (about 700Mb of the compressed file). I am studying the RNA-seq data and trying to map the reads on chromosome A1 for now, using the following command:

hisat2 -p 4 --dta-cufflinks -x ${hisat2Ref} \
       -U fastq/ERX2234749.fastq.gz |
       samtools view -bh - |
       samtools sort - > bam_cuff/ERX2234749.bam

, but I have the following Error:

Error reading _rstarts[] array: 483248, 485832
Error: Encountered internal HISAT2 exception (#1)
Command: /home/asus/anaconda3/envs/bioinformatics/bin/hisat2-align-l --wrapper basic-0 -p 4 -q -x hisat2_index2/TA1 --read-lengths 151 -U /tmp/5387.unp 
(ERR): hisat2-align exited with value 1
[main_samview] fail to read the header from "-".
samtools sort: failed to read header from "-"

I use Ubuntu 20.4. Any advice? Many thanks in advance.

[ATpoint]

Is the input really in /tmp so in the memory?

[Laila]

If I understand what is /tmp well (files found in the temporary directory), I will say all my inputs are found in the same directory I run the command in.