This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Building bowtie2 index out of igc

I'm trying to build an index out of the IGC reference (http://meta.genomics.cn/metagene/meta/home) using the bowtie2-build command. When the process is done, the output of the bowtie2-inspect command is: bowtie2-inspect: bt2_inspect.cpp:234: void print_ref_sequences(sdt::ostram&, bool, const EList<std::basic_string<char, std::char_traits<char="">, std::allocator<char> >, 128>&, const TIndexOffU*, const std::string&): Assertion 0 failed. Aborted (core dumped)

Obviously, the index file wasn't created properly so there's no use trying to align reads according to it. But a can't see what went wrong. I need help figuring out how to make it right.

Thanks for the help.

next-gen sequencing igc
• 1,980 views • link
written by uriamo • uriamo

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Issues with vg surject into paths
    written by Rugare • Rugare
    Hello, I essentially am aiming to calculate the mean mapping qualities of patient FASTQs to different ethnicity genomes in the pangenome. HG1109 is one of …
  • vgconstruct crashes
    written by Uveyik • Uveyik
    I am running following command vg construct -C -r chr1.fasta -v chr1.vcf.gz -t 1 -m 32 > human_v38.chr1.vg with the following error terminate called after …
  • Dsuite Dinvestigate error but no indication as to the source
    written by Drew • Drew
    Can anyone tell me what this error code is saying? ``` There are 3 sets (populations/species) excluding the Outgroup /builddir/build/BUILD/gcc-11.4.1-20230605/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/basic_string.h:1040: std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, …
  • Problem with vg autoindex with phased VCF
    written by mirko1998coggi • mirko1998coggi
    Hi, I'm trying to use `vg autoindex` with the human Chromosome 17 using: - `Homo_sapiens.GRCh37.dna.chromosome.17.fa` as REF (downloaded from Ensembl at [1]) - `ALL.chr17.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz` as …
  • error:[Surjector] could not identify path position of surjected alignment
    written by LilithElina • LilithElina
    This question is a kind of follow-up to [this one](https://www.biostars.org/p/420687/). I am trying to convert a GAM file output from `vg map` to BAM for …
  • bam-readcount installation problem: Linking CXX executable
    written by user31888 user31888
    I am trying to filter false positives from a VarScan2 somatic variant call using the fpfilter program. For that I need to install bam-headcount, but …
  • Error compiling Reapr
    written by Prakki Rama Prakki Rama
    Hi all, I get this error when I compile Reapr tool. May I know if anyone experienced this before and suggest me some solution. ------------------------------------------------------------------------------ …
  • bowtie could not build the index
    written by zizigolu zizigolu
    Sorry guys, I was building transcriptome index: I have `yeast_SGD_anno.gtf` and `orf_coding.fasta` as input which are in bowtie2 folder, then I typed: ``` [izadi@lbox161 bowtie2-2.2.5]$ …
  • Tophat2 Error With Repeat-Masked Genome!!
    written by Rahul Sharma Rahul Sharma
    <p>Dear all,</p> <p>I was trying to <strong>map</strong> the <strong>RNA seq data</strong> on the <strong>assembled genome</strong>. I was using Tophat <code>tophat-2.0.10.Linux_x86_64</code> and Bowtie2 <code>bowtie2-2.1.0</code>. When I …
  • Error Installing Cufflinks
    written by lin.barnum • lin.barnum
    <p>I am trying to install Cufflinks on Ubuntu 11.10 and and running into the following error which I cannot figure out. What am I missing …