(ERR): hisat2-align died with signal 11 (SEGV) (core dumped) about hisat2 HOT 13 CLOSED

I get the same error using one of the pre-built indices (H. sapiens, Ensembl GRCh38, genome_tran)

from hisat2.

Please try the newest version of HISAT2 - this problem might have been fixed. I'll close the issue and reopen if the problem still exists.

from hisat2.

I too am getting the same error:

• OS: 64-bit Linux (cluster)
• HISAT2 version: build from source GitHub master of 01-27-16
• Indices: Pre-built H. sapiens genome_tran (Ensembl GRCh38) downloaded on 01-27-16 from HISAT2 website
• Input reads: fastq.gz files for quality-trimmed Illumina 101 base, paired, stranded RNA sequencing reads
• Command: hisat2 -p 24 -1 trimmed_paired_1.fastq.gz -2 trimmed_paired_2.fastq.gz -q --phred33 --rna-strandness FR -x genome_tran -S eg.sam
• Error: (ERR): hisat2-align died with signal 11 (SEGV)

from hisat2.

I've been trying to replicate this issue, but no success so far. Would it be possible for you to provide me a small subset of the reads so that I can reproduce and fix the problem?

from hisat2.

Hi Daehwan,
I downloaded the lastest HISAT2 binary, I get the same error. The index step goes well, the error comes while aligning. Any clues?
Thanks

from hisat2.

I encountered same error with 1 set of paired end reads of size 2 GB that is quality trimmed with minimal length of 70.
Following is the error:
(ERR): hisat2-align died with signal 11 (SEGV) (core dumped)
Machine specification: OS: 64-bit Linux, 16 GB RAM, 4 core processor
Hisat2 works fine with other datasets except for one.

Is this because of different read length for a given pair of read post trimming? If so, how should I handle it to dodge the error ?

Thanks

from hisat2.

Different read lengths should work fine. In order to fix this problem, it's always good for me to have a test data set. Would you be able to share your reads with me? If so, please send me email at [email protected]. I'll provide you instructions to upload your data into our FTP server.

from hisat2.

Ok I think I had my issue resolved but not sure how. The problem was due to indexing. My initial reference had pseduomolecules and unassembled contigs. I removed the unassembled contigs and then indexed again using hisat2-build and it worked!. May be it would useful to have more descriptive errors logs in the output of failed runs. Thanks

from hisat2.

Re: my comment from 7 days ago:

When I run the command multiple times, the HISAT2 run gets aborted at exactly the same point every time. The SAM file is ~24 GB at that point (input fastq.gz files are ~1.8 GB). The last four lines of the SAM files:

D8LSZMS1:142:C6WM3ACXX:1:2107:14625:72909   339 3   184182218   1   31M508N58M  =   184182046   -261    ACAAGGCCAGCGAGAATGCCATCGTGTGGAAGATCAAGCGCATGGCAGGCATGAAGGAATCGCAGATCAGCGCAGAGATTGAGCTTCTG   CDDDDDCDDDDDEDDDDDDDDDDDDAEEEEEEEFFFFHHJJJJJJJJJJIJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJH   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:89 YS:i:0  YT:Z:CP XS:A:+  NH:i:2
D8LSZMS1:142:C6WM3ACXX:1:2107:14625:72909   419 3   184182046   1   2M103N87M   =   184182218   261 AGGTGAGGATCCCAACCCCACTGAACACAAGCGGGGTGCAGGTGATCTGCATGAAGGGGAAGGCCAAGTACAAGGCCAGCGAGAATGCC   HJJGHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAB@DDDBDDDEEDDDDDDDDDDDDDDDDDDDDCCDDDDDDDDDDDDDDDDDDD   AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:89 YS:i:0  YT:Z:CP XS:A:+  NH:i:2
D8LSZMS1:142:C6WM3ACXX:1:2107:13791:72974   81  1   228320658   255 10S79M  =   228320662   102 CTTTCTTACTTTCCATTCCATTCATCCATCCATCTACTATCCATCTGCCACTCCTGCACCTGTTCACCTGTTCATTCATTTATCTGTCA   CDDDCCCA5;:DDDEDDECCCDFFDBHHHE?@@@D=CGHFGIGGGIIGGGIGJIJIIHGJJJIGGGFIJJIJIJIJJJIIJJJFJIJIG   AS:i:-10    XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:79 YS:i:-1 YT:Z:DP XS:A:+  NH:i:1
D8LSZMS1:142:C6WM3ACXX:1:2107:13791:72974   161 1   228320662   255 88M1S   =   228320658   -102    ATTCCATTCATCCATCCATCTACTATCCATCTGCCACTCCTGCACCTGTTCACCTGTTCATTCATTTATCTGTCAGCCTGTTTACCCAG   HIJJIIIHEHJIFIIJJJJAFGIJJJJJJJJDGHIGIHFGGIIIJJDEFEHIIIJEHIJJIIEHIJJ

I can share the fastq.gz files with you if you still haven't managed to get raw data for replication.

Edited to add note: The fastq.gz files work fine with Tophat or Subread.

from hisat2.

@ashipde, would you like to send me an email ([email protected])? I'll provide you instructions how to upload the reads.

from hisat2.

@ashipde, thank you for providing me the data! I just fixed the issue. Please let me know if you have any other questions.
I'll close this issue, and I'd like to suggest other users to open a new issue if they still have a similar issue, and I'll appreciate if they provide some data so that I regenerate and fix a problem.

from hisat2.

hisat2 -x genome-scaffolds.abyss.77.gc.ov31.5kb.masked -1 read1.fq.gz -2 read2.fq.gz -S test.sam --rna-strandness FR

the command above fails with the following error:
(ERR): hisat2-align died with signal 11 (SEGV)

I am using the latest version from github.

The following is the log from the hisat2-build
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps

from hisat2.

I'm having the same problem with the reference sequence with only gaps. That is just a warning though, shouldn't alter the process!

from hisat2.