Bracken

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I always have a segmentation fault when trying to build a krakenuniq database into bracken.. Any help will be appreciated. **(krakenuniq) [user@server bracken_testing]$ bracken-build -d krakenuniq_db/ -t 16 -k 31...

jalalsiddiqui

Bracken read length for ITS1 amplicons

1

Hi, I have analysed ITS1 amplicons from fungal samples (leaf endophytes) using kraken2 and the PlusPFP-16 indices provided by Ben Langmead. These amplicons were trimmed for PCR primer sequences, but...

ARW-UBT

Question about calculations and intersample comparison

1

Hey Jennifer! First of all, thanks for the tool and the support you provide to users. I have a question regarding how things are calculated in Bracken. I understand that...

alanxelena

Hi Developers, I am installing Bracken with this code: bash install_bracken.sh But it returns: chmod: cannot access \u2018bracken-build\u2019: No such file or directory Please kindly give me instructions on how...

YutongLi5276

Lower nr of reads at Class compared to Order level Bracken

8

Hi, I was using Bracken to re-estimate reads at Class level for Eukaryotes. Now, there is a certain fish Order that I don't want included in the general fish Class,...

CETHuyghe

Segmentation fault in STEP 4: CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS

32

I built a Kraken1 database and I'm trying to generate the corresponding bracken distribution file. Everything went well until I got a segmentation fault at STEP 4 (CONVERTING KMER MAPPINGS...

thbtmntgn

Hi, I left this issue as a comment on someone else's similar issue, but wanted to open up my own issue as well. I am experiencing an issue in step...

ulin27

bracken 2.9 build error

3

Hellow,I followed the correct procedure to build a standard database using Kraken2. However, when running bracken-build, I encountered the following error: >> Selected Options: kmer length = 35 read length...

0russ4

Segmentation fault and Missing separate debuginfos

1

### error Program terminated with signal 11, Segmentation fault. #0 0x0000000000407260 in ?? **()** Missing separate debuginfos, use: debuginfo-install coreutils-8.22-18.el7.x86_64 (gdb) bt #0 0x0000000000407260 in ?? () #1 0x0000000000407d2a in...

Zhenghong-Wang

Malformed fasta file

8

While running what is listed as "Step 2a" in the Running Braken guide, I get the following error: > classify: malformed fasta file - expected header char > not found...

sturne29