Comments (13)
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.
Related Issues (20)
- A question about methylation information extraction
- Any plans to support Apple Silicon architecture? HOT 1
- Installation Issue Error 1 - make HOT 1
- -np argument seemingly not working
- ERR): "fastq file.fastq" does not exist. Exiting now ...
- [Bug Report] hisat2-align exited with value 137, space complexity of hisat2
- hisat2 location does not exist
- Hisat-3N mapping quality
- hisat2-build index for circRNA-seq
- hisat2-build failed for Segmentation fault
- [Future request] hisat-3n table option to report conversions summarized to genomic feature or reads counts
- Issue with hisatgenotype HOT 1
- Mapping using different parameters --very-sensitive and default
- (ERR): "ref.genome" does not exist Exiting now ...
- --directional-mapping-reverse vs. --rna-strandness on HISAT3N
- Question about calculation of base counts in hisat3Ntable
- mkfifo failed error and change $temp_dir HOT 1
- Question about Hisat-3N align
- Support Third-generation full-length RNA-seq?
- Enabling a --temp-directory parameter
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hisat2.