failed to build index mm10

[Kiliankleemann]

Hello, I downloaded the mm10 index from Bowtie2 website and ran make_mm10.sh

Everything seems to run fine until the end when it just says "failed to build and index"

Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:29 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:20 bmax according to bmaxDivN setting: 663195875 Using parameters --bmax 497396907 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 497396907 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:01:28 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:24 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:38 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 2.65278e+09 (target: 497396906) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 2652783500 for bucket 1 (Using difference cover) Index building failed; see error message

I'm not sure were to look for the error and how to fix it. Do you have any recommendations?

[ch4rr0]

Hello,

what version of bowtie2 are you using and what were your command line arguments?

[Kiliankleemann]

Dear Ben,

bowtie2 version: 2.4.2

Command: mkdir SAM_files cat sample_list.txt | while read sample; do bowtie2 -p 12 -q --local -x mm10 -1 fastq/trimmed_reads/${sample}.1.trimmed.fastq.gz -2 fastq/trimmed_reads/${sample}.2.trimmed.fastq.gz -S SAM_files/${sample}.unsorted.sam done

Everything seems to be working ok until the final step:

Index building failed; see error message.

I tried to find the error message but could not find anything.

I have re-downloaded everything and I’m confused because online i read that the bt2 files are already the premade index which can be directly used but then there is also the make_mm10 shell script.

I would be super happy if you could give me some tipps.

Kind regards Kilian

On Nov 15, 2021, at 1:16 PM, ch4rr0 @.***> wrote:

Hello,

what version of bowtie2 are you using and what were your command line arguments?

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