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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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Nothing to be done #4

Closed wjyzidane closed 6 years ago

wjyzidane commented 6 years ago

Salmon TE runs well on my previous samples but when I run it again today. It is done with nothing output.

image

So I wonder if anything is going wrong. Thanks!

hyunhwan-jeong commented 6 years ago

I guess this was because all the outputs were created so SalmonTE skipped the quantification. Could you remove or change name of the previous output folder?

wjyzidane commented 6 years ago

After I delete the previous folder. The SalmonTE runs well without error info. But there is still no result in the output folder. See my command, process info and output as below:

qq20180101-1

qq20180101-2

qq20180101-3

qq20180101-4

Thanks and Happy New Year!

hyunhwan-jeong commented 6 years ago

You can specify the output directory with --outpath parameter. Could you please run the below command?

./SalmonTE.py quant --reference=hs $file --outpath=test_SalmonTE_output

You will see your output files in test_SalmonTE_output directory. If you still can't solve the problem once you run the command then I will need your information to figure out the issue:

Happy New Year!

Hwan

wjyzidane commented 6 years ago

Hi Hwan,

I found the problem. It is suffix. Because my filename is test.fq. When I changed it to test.fastq, it runs well. Thanks a lot!

Jingyi

hyunhwan-jeong commented 6 years ago

Thanks for your report. I think people oftentimes use .fq suffix, so the suffix will be supported in next version of SalmonTE. I will close the issue and let you know once I will update it.

Thank you,

Hwan

wjyzidane commented 6 years ago

Thank you!

hyunhwan-jeong commented 6 years ago

@wjyzidane,

I have committed 1950aaf7098c3bc39448d51e8b9711ee89dd28e9, andn now SalmonTE supports fq and fq.gz extensions. Please let me know if it does not work for you.

Hyun-Hwan Jeong

wjyzidane commented 6 years ago

Thanks so much!

Jingyi

在 2018年6月4日，下午1:03，Hyun-Hwan Jeong notifications@github.com 写道：

@wjyzidane https://github.com/wjyzidane,

I have committed 1950aaf https://github.com/hyunhwaj/SalmonTE/commit/1950aaf7098c3bc39448d51e8b9711ee89dd28e9, andn now SalmonTE supports fq and fq.gz extensions. Please let me know if it does not work for you.

Hyun-Hwan Jeong

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