Hisat2 Error

Question

[Forough]

Hello everyone,

In order to align the RNA- seq reads to the genome I faced this error:

Could not locate a HISAT2 index corresponding to basename "../../Index/hg38"
Error: Encountered internal HISAT2 exception (#1)
Command: /usr/bin/hisat2-align-s --wrapper basic-0 --dta -x ../../Index/hg38 -S sra1.sam -U sra_data.fastq 
(ERR): hisat2-align exited with value 1

The command that I entered for alignment is as below:

hisat2 --dta -x ~/apps/Proj/Index/hg38 -U sra_data.fastq -S sra1.sam

I would be appreciate if you help me to solve it.

Thanks in advance

[cpad0112]

what is the output from ls -l ~/apps/Proj/Index/hg38? Check folder permissions and index is complete.

[Forough]

thank you for your response, it is as below:

total 4554772 
-rw-rw-r-- 1 genetics genetics 1020663384 نوْوامبر 20  2015 genome.1.ht2
-rw-rw-r-- 1 genetics genetics  762328952 نوْوامبر 20  2015 genome.2.ht2
-rw-rw-r-- 1 genetics genetics      15065 نوْوامبر 19  2015 genome.3.ht2
-rw-rw-r-- 1 genetics genetics  762328946 نوْوامبر 19  2015 genome.4.ht2
-rw-rw-r-- 1 genetics genetics 1342456349 نوْوامبر 20  2015 genome.5.ht2
-rw-rw-r-- 1 genetics genetics  776249234 نوْوامبر 20  2015 genome.6.ht2
-rw-rw-r-- 1 genetics genetics          8 نوْوامبر 19  2015 genome.7.ht2
-rw-rw-r-- 1 genetics genetics          8 نوْوامبر 19  2015 genome.8.ht2
-rwxrwxr-x 1 genetics genetics       1292 نوْوامبر 20  2015 make_hg38.sh

[cpad0112]

are you the user genetics? It seems you have used path: "../../Index/hg38" (as understood from error log "Could not locate a HISAT2 index corresponding to basename "../../Index/hg38"). Can you try below command and post error? You are supposed to provide basename of the index.

hisat2 --dta -x /home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam

Please check this path (/home/genetics/apps/Proj/Index/hg38/) and it should have genome indices.

[Forough]

I entered below command:

hisat2 --dta -x ~/home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam

this error appeared:

Could not locate a HISAT2 index corresponding to basename "/home/genetics/home/genetics/apps/Proj/Index/hg38/genome"
Error: Encountered internal HISAT2 exception (#1)
Command: /usr/bin/hisat2-align-s --wrapper basic-0 --dta -x /home/genetics/home/genetics/apps/Proj/Index/hg38/genome -S sra1.sam -U sra_data.fastq 
(ERR): hisat2-align exited with value 1

[cpad0112]

I suggested to run hisat2 --dta -x /home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam and instead you executed hisat2 --dta -x ~/home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam. That is incorrect. Please run as suggested otherwise, issue will be difficult to troubleshoot.

`

Answer 1

[sure]

The path you're specifying is not correct. Look carefully at the expanded path.
Input Code:

hisat2 --dta -x ~/home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam

the ~/home/genetics/apps/Proj/Index/hg38/genome gets expanded to /home/genetics/home/genetics/apps/Proj/Index/hg38/genome .

~ is causing the issue. remove that and rerun it. The correct input should be

hisat2 --dta -x /home/genetics/apps/Proj/Index/hg38/genome -U sra_data.fastq -S sra1.sam

[Forough]

Dear friend, I used your recommended command, but I got this error:

Killed
(ERR): hisat2-align exited with value 137

[cpad0112]

Try to increase the memory allocated and also check if your fastq records are in correct format.

Answer 2

[sure]

That is most likely a RAM issue. How much memory you are using? Whatever you are specifying most likely it is not enough. Increase the allocated memory.