problem with tophat

Ariuka · 03-27-2012, 04:50 PM

Hi, guys. I am completely newbie in this sequencing field.

I just started using tophat. I installed everything. However, while tophat was mapping my reads, it gave me this error (I am following protocol of tophat and cufflinks- http://www.nature.com/nprot/journal/....2012.016.html)

My command was:

$ tophat -p 8 -G genes.gtf -o C1_R2_thout genome C1_R1_1.fq C1_R1_2.fq

Error:

[Tue Mar 27 17:12:31 2012] Processing bowtie hits
Traceback (most recent call last):
File "/home/bitl/software/bin/tophat", line 3063, in <module>
sys.exit(main())
File "/home/bitl/software/bin/tophat", line 3029, in main
user_supplied_deletions)
File "/home/bitl/software/bin/tophat", line 2646, in spliced_alignment
right_reads_map = maps[1].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'

I am using Ubuntu 11.10, 64 bit.

Is it because of RAM? cause mine is only 4GB. I ordered 16GB RAM, expecting soon.

Thank you for your time ^^

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03-27-2012, 04:50 PM	#1
Ariuka Junior Member Location: South Korea Join Date: Mar 2012 Posts: 1	problem with tophat Hi, guys. I am completely newbie in this sequencing field. I just started using tophat. I installed everything. However, while tophat was mapping my reads, it gave me this error (I am following protocol of tophat and cufflinks- http://www.nature.com/nprot/journal/....2012.016.html) My command was: $ tophat -p 8 -G genes.gtf -o C1_R2_thout genome C1_R1_1.fq C1_R1_2.fq Error: [Tue Mar 27 17:12:31 2012] Processing bowtie hits Traceback (most recent call last): File "/home/bitl/software/bin/tophat", line 3063, in <module> sys.exit(main()) File "/home/bitl/software/bin/tophat", line 3029, in main user_supplied_deletions) File "/home/bitl/software/bin/tophat", line 2646, in spliced_alignment right_reads_map = maps[1].unspliced_bwt AttributeError: 'list' object has no attribute 'unspliced_bwt' I am using Ubuntu 11.10, 64 bit. Is it because of RAM? cause mine is only 4GB. I ordered 16GB RAM, expecting soon. Thank you for your time ^^