Tophat2 stucked

[Joshua_HIT]

Hi:

I want to run tophat2 on four sets of data(human chimp gibbon gorilla). For human I downloaded hg19 from USCS in which Bowtie2 index has been included, so human has been finished successfully. but for other three spices I have to use "bowtie2-build refgene.fa genome" to build index on my own.

the problem is: for all index established by me, tophat2 can not run successfully!! It will stucked on process below:


[2013-12-07 18:26:04] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-12-07 18:26:04] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-12-07 18:26:04] Checking for Samtools
Samtools version: 0.1.19.0
[2013-12-07 18:26:04] Checking for Bowtie index files (genome)..
[2013-12-07 18:26:04] Checking for reference FASTA file
[2013-12-07 18:26:04] Generating SAM header for ../../Bowtie2_Index/Chimp/chimp
format: fastq
quality scale: phred33 (default)
[2013-12-07 18:26:57] Preparing reads
left reads: min. length=101, max. length=101, 81784737 kept reads (75486 discarded)
right reads: min. length=101, max. length=101, 81747073 kept reads (113150 discarded)
[2013-12-07 19:48:52] Mapping left_kept_reads to genome chimp with Bowtie2

2 hours have passed... and nothing changed. I have not seen any error on any action before...I think the problem are bowtie indexes I build.

[GenoMax]

If you have a large data set then it is not unusual to have the job run for several hours (2 hr is not a lot).

Have patience. As long as the process is running no need to worry.

[dpryan]

If you want RNAseq reads aligned more quickly then you need to use something like STAR (though it requires MUCH more RAM).

[Joshua_HIT]

If you have a large data set then it is not unusual to have the job run for several hours (2 hr is not a lot).

Have patience. As long as the process is running no need to worry.

you are totally right. I am a new freshman on biology, I indeed need more patient! Thanks!!

[Joshua_HIT]

If you want RNAseq reads aligned more quickly then you need to use something like STAR (though it requires MUCH more RAM).

Thanks for your advise. I would have a look on that!