Tag: bowtie2-align

Bowtie2: Error, fewer reads in file specified with -1 than in file specified with -2 1 Hi all, This is my first time attempting to align sequences to a reference index. I am using bowtie2 with the -1 and -2 arguments and have gotten the following error message: Error, fewer…

Hello! I am working on assembling a transcriptome of the terminal ganglion of the cricket (Gryllus bimaculatus). We are working on a non-model species and thus did not remove ribosomal contamination during library prep. We want to remove ribosomal contamination bioinformatically, and I am mapping our sequences, which have been…

Bowtie Parameter Switch Error 1 I’m having this problem when running bowtie2 and can not figure it out. I am running a fairly basic bowtie2 command shown here bowtie2 –very-sensitive -x /usr/lusers/achits/achits/genomes/Xtropicalis9/Xtropicalis9 -1 z1.fastq -2 z2.fastq -X 2000 -p 14 -S and for some reason the error I’m getting is…

trying to look the version of the programs under miniconda3 directory 0 Hello, I had to uninstall miniconda3 on my previous HPC. The point is that I made a backup of the miniconda3 directory where all my programs and environments are. Is there a way to see the version of…

bowtie2 – (ERR): bowtie2-align exited with value 13 1 I am trying to run bowtie2. but following error are occuring everytime bowtie2 –very-fast-local -x bowtie -q -1 R1.fastq -2 R2.fastq -s aligned.sam Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of ‘int’ Aborted…

Use RSEM and Bowtie2 to align paired-end sequences 0 I want to use rsem-calculate-expression and bowtie2 aligner to align paired-end sequence based on the following conditions: 2 processors generate BAM file very fast bowtie2 sensitivity append gene/transcript name My code: rsem-refseq-extract-primary-assembly GCF_000001405.31_GRCh38.p5_genomic.fna GCF_000001405.31_GRCh38.p5_genomic.primary_assembly.fna rsem-prepare-reference –gff3 GCF_000001405.31_GRCh38.p5_genomic.gff –bowtie2 –bowtie2-path /bowtie2-2.4.5-py39hd2f7db1_2 –trusted-sources…

Question: Question: bowtie2-align-s: error while loading shared libraries Abhinav26 days ago Question: bowtie2-align-s: error while loading shared libraries /home/emilyw/.conda/envs/shotgun_134/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed! Exiting…

Hello, I ran seqtk seq -VQ64 read1.fastq.gz > read1_phred33.fastq to convert my 64 based phred score reads to 33 based phred score phred reads. However when I attempted to run them through tophat alignment I got this error: Saw ASCII character 4 but expected 33-based Phred qual. terminate called after…

Weird error from BWA and BOWTIE2 1 Hi community, Recently I have used BWA and Bowtie2 to align simulated DNA sequencing data to test our sequencing simulator. I got some errors from both aligners: BWA: submit.sh: line 48: 6881 Segmentation fault (core dumped) BOWTIE2: terminate called after throwing an instance…

(ERR): bowtie2-align died with signal 24 (XCPU) (core dumped) 0 Hi all, it is my first time using bowtie2, and I have a problem. I conducted the following command for reads mapping: bowtie2 -q –local -x mm10 -U SRR5839956_trimmed.fq -S SRR5839956.sam It created a 600MB sam file then come with…