Question: Help with Tophat2 run
0
gravatar for Neu
28 days ago by
Neu10
India
Neu10 wrote:

Hi, I am getting the error as below when trying to run tophat2. Please help me to resolve this. command:

tophat2 -o tophat_fusion --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search mm10 R1.fastq R2.fastq
[2019-03-25 15:14:08] Preparing reads
   left reads: min. length=35, max. length=100, 71915041 kept reads (86999 discarded)
  right reads: min. length=35, max. length=100, 71830791 kept reads (171249 discarded)
[2019-03-25 15:45:04] Mapping left_kept_reads to genome mm10 with Bowtie 
  [FAILED]
Error running bowtie:
Error while flushing and closing output
Command: /usr/bin/bowtie-align-s --wrapper basic-0 -v 2 -k 20 -m 20 -S -p 1 --sam-nohead --max /dev/null mm10 - 

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
  
ADD COMMENTlink modified 28 days ago by h.mon24k • written 28 days ago by Neu10
1

Check your RAM and disk space left. Then try to remove bowtie1 parameter

Related :

http://seqanswers.com/forums/showthread.php?t=15599

ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2

ADD REPLYlink modified 28 days ago • written 28 days ago by Bastien Hervé4.0k

I have 300 GB space available and the PC has 96 GB of RAM. How can I install older version of bowtie2? I am trying it by running apt-get bowtie2=2.2.1, but it is not working. The version 2.3.4.1 is getting downloaded with tophat2. Thank you

ADD REPLYlink written 28 days ago by Neu10

If you have bowtie2 installed, just don't use the --bowtie1 parameter

Default bowtie version used is bowtie2

ADD REPLYlink modified 28 days ago • written 28 days ago by Bastien Hervé4.0k

I will be using tophat2-fusion which needs bowtie1 index (https://circexplorer2.readthedocs.io/en/latest/).

ADD REPLYlink written 28 days ago by Neu10

Would you please try the option to check if this is the source of the error.

I also see in the docs that STAR is an other option to align your paired end reads, if you have it on your PC I highly suggest you to try it.

STAR --chimSegmentMin 10 --runThreadN 10 --genomeDir hg19_STAR_index --readFilesIn read_1.fastq read_2.fastq
ADD REPLYlink written 28 days ago by Bastien Hervé4.0k

Yes I will surely try that. I am intentionally avoiding star as I can not perform de Novo assembly study with that. Thank you,

ADD REPLYlink written 28 days ago by Neu10

Try updating SAMtools

ADD REPLYlink written 28 days ago by Kevin Blighe41k
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