Error during runing alignment .

[sdabral05]

I am using hisat2 version 2.1.0.

Command i using - 1 - For indexing hisat2-build /index/Hg38_new.fa HG38

2 - For alignment - hisat2 -p 8 --dta -x HG38 -1 sample_1.fastq.gz -2 /sample_2.fastq.gz -S sample1.sam

Error I am facing -

Error while flushing and closing output terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

I am also getting sam file with a size of 4.3 gb and my raw file size is sample_1 = 1.5 gb and sample_2 = 1.7 gb .

I don’t know what’s this error means and this sam file is a correct file or not.

Please help me to find out the solution .

[parkchanhee]

Could you check a free disk space or quota limit?

[sdabral05]

I have 1 tb free disk space.

[parkchanhee]

In most cases, this error occurs when hisat2 can't write the output file to disk.

Free disk space, file write permissions, network problems if storage is connected via a network, can cause a problem.

If you have enough disk space, try using shell redirection instead of -S option.

hisat2 -p 8 --dta -x HG38 -1 sample_1.fastq.gz -2 /sample_2.fastq.gz > sample1.sam

[sdabral05]

I try this also I am getting same error .

[sdabral05]

Error is resolve there is some problem with hard disk i try the with another hard disk with same free space and its work properly.

Do you have any idea why hard disk with same free space of same company not working properly ?

[dnebdal]

You probably want to ask somewhere more specific to your OS - this sounds like an operating system/file system problem more than anything hisat2 specific?

[sdabral05]

hi ,

In my case i have 3.3 gb.gz file which produce 24gb sam file .So if you are not seen any error during and after running than you have a correct sam file.

Thanks and Regards Shruti Dabral

On Thu, Apr 9, 2020 at 1:42 AM RogerioRibeiro201505534 < notifications@github.com> wrote:

@sdabral05 https://github.com/sdabral05 just of curiosity, what was the size of your sam file in the end? When I run hisat on my pair end data I get the same error. My input files are around 1.5Gb (each, for a total of 3Gb) and my sam file is at least 16GB. I already concluded my issue has to do with the size of my output, but I´m unsure if the 16GB sam fille is normal.

Comands

Index

hisat2-build --seed 1 -p 4 -f catharanthus_genome_v2/cro_v2_asm.fasta results/cro_index

software/hisat2-2.2.0/hisat2 -q --rna-strandness FR --pen-noncansplice 3 --pen-canintronlen C,0.0,1.0 --pen-noncanintronlen C,-8.0,1.0 --dta -p 4 -x results/cro_index --summary-file -1 /RNAseqdata/lane1/idio/sample_1/R1_cut_paired.fastq.gz -2 /RNAseqdata/lane1/idio/sample_1/R2_cut_paired.fastq.gz -S results/alignments/idio/idio_1.sam

Best!

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[mzinkgraf]

Hi, I am getting a similar error message using version 2.2.0 and my server (Ubuntu 18.04.2 LTS) should not be impacted by space or memory issues 5Tb available space and 780Gb memory.

hisat2 -p 4 --dta -x L_crocea -q $DATA/quality_control/SRR1964649_1.scythe.sickle.fastq.gz -S sam/SRR1964649.sam Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

Thanks Z

[parkchanhee]

Hi, @mzinkgraf

You need to specify the '-1 ... -2' or '-U' option. If you want run with single-end read, use -U option. ex> hisat2 -p 4 --dta -x L_crocea -q -U $DATA/quality_control/SRR1964649_1.scythe.sickle.fastq.gz -S sam/SRR1964649.sam

Thanks Chanhee

[mzinkgraf]

Hi @parkchanhee

Thanks for the suggestion but that produces a new error.

hisat2 -p 4 --dta -x L_crocea -q -U $DATA/quality_control/SRR1964649_1.scythe.sickle.fastq.gz -S sam/SRR1964649.sam sh: 1: Syntax error: ")" unexpected (ERR): hisat2-align exited with value 2

The file works just fine when uncompressed but fails when compressed with gzip

[mzinkgraf]

The gzip error seems to be specific to these GitHub builds for V2.2.0 and V2.1.0.

The Linux x86_64 binary for V2.1.0 from https://ccb.jhu.edu/software/hisat2 successfully runs with gzipped fastq files

UPDATE: The run is also successful when I build hisat2 v2.2.0 from the source code available through the DaehwanKimLab releases.

[Ramsha12-star]

Help me to solve this Hisat2 error. I have disk space 238GB

hisat2 -x thal.fa -1 /mnt/g/reads/ERR463424303_1.fp.fq.gz -2 /mnt/g/reads/ERR463424303_2.fp.fq.gz --dta -S ERR463424303.sam

Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

[najibveto]

Help me to solve this Hisat2 error. I have disk space 238GB

hisat2 -x thal.fa -1 /mnt/g/reads/ERR463424303_1.fp.fq.gz -2 /mnt/g/reads/ERR463424303_2.fp.fq.gz --dta -S ERR463424303.sam

Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

hello, sorry to ask, did u solve the problem? i have same problem with my data. thank u.

[HasiHays]

I have this error for a file that does not exist. it's already there.

hisat2 -p 8 --dta -x data/index/genome -1 data/nfu/nfu_1.fastq -2 data/nfu/nfu_2.fastq -S nfu.sam

(ERR): Read file 'data/nfu/nfu_1.fastq' doesn't exist Exiting now ...

Any idea what to do

[jaberdehghani]

I got the following error during the conversion of my fastq file to sam. Does anybody has a solution? Thank you in advance.

Error: Read SRR14085440.33094376 K00208:YA018:4:2105:2608.24:961.58 length=51 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

[moobashara]

i am getting the file doesnot exist error while running the hisat2 in terminal