Error while using hisat2 (hisat2-align exited with value 137)

Question

[szabo.marton]

Dear All,

I've tried mapping my trimmed RNA-Seq reads against the indexed reference genome using hisat2 but I've got the following error message:

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

I coudn't find any answers related to this type of error. Here is the used command:

hisat2 -x Rno_index --known-splicesite-infile rno6_splice_sites.txt -1 S459_R1_paired.fastq.gz -2 S459_R2_paired.fastq.hisat2 -x Rno_index --known-splicesite-infile rno6_splice_sites.txt -1 S459_R1_paired.fastq.gz -2 S459_R2_paired.fastq.gz | samtools view -bS - > SIR_1.bam

I've followed the workflow provided by the Babraham Bioinformatics

For the mapping I've biuld my own indexed genome using hisat2-build from the Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa reference genome, obtained from Ensembl. Also I've tried with the already indexed rat genome from Ensembl, but without any succes.

Before mapping the very first step was merging the individual sequencing runs from the same samples with cat file_1R1.fastq file_2R1.fastq.gz > file.fastq.gz then I've performed adapter trimming:

java -jar /home/Documents/Trimmomatic-0.38/trimmomatic-0.38.jar PE S458_R1.fastq.gz S459_R2.fastq.gz S459_R1_paired.fastq.gz S459_R1_unpaired.fastq.gz S459_R2_paired.fastq.gz S459_R2_unpaired.fastq.gz HEADCROP:15 CROP:55 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:36

Any idea about what did I wrong are appreciated.

[GenoMax]

How much memory do you have available? Are you running this under a job scheduler? Your job is getting killed so you are likely exceeding some resource allocation.

[szabo.marton]

Thank you for your reply! Would it be that simple? I have only 4 Gb RAM, it is not to much but it was enough for previous analysis. I don't use any job scheduler, would it be useful?

[GenoMax]

4 GB RAM is not enough to be able to align rat genome with pretty much any NGS aligner.

[szabo.marton]

Could it help if I double the RAM or should I use a better computer?

[GenoMax]

Find better hardware if you can. If you can't then doubling RAM may allow you to use bwa.

[szabo.marton]

I've double the RAM and now it's working perfectly

[kongyunhui1]

I have the same problem, but i think may it was not the limited RAM caused this situation, because my severs has 2T ram, when i run hisat2, it successful ran at former 4 sample, but when face a strange sample, the memory was ran up fast and the machine become very slow, then "Killed (ERR): hisat2-align exited with value 137" happend

[iamsmor]

Hello ı have same problems too. I am trying align my trimmed data

hisat2 -q -x $RNA_REF_INDEX/genome_snp_tran -U $RNA_DATA_DIR/SRR309133.fastq.gz -S SRR133309.sam

ı am using human grc38_snp_tran.gtf for ref but ı got same error

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

ı dont know how ı can double my memory for this jop? ı will be grateful for any help.