Help with Tophat2 run

Question

[Neu]

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
  

[Bastien Hervé]

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

[Neu]

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

[Bastien Hervé]

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

Default bowtie version used is bowtie2

[Neu]

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

[Bastien Hervé]

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

[Neu]

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

[Kevin Blighe]

Try updating SAMtools

[h.mon]

To install bowtie1, use apt-get install bowtie.