UnicodeDecodeError

[wjyzidane]

Hi hyunhwaj,

Previously, SalmonTE works fine for me but recently when I run the program, it gives the error as below and any comments?

~/software/SalmonTE-master/SalmonTE.py quant --reference=m S17_R1_001.fastq.gz S17_R2_001.fastq.gz

Jingyi

[wjyzidane]

Btw, if I use this command, it gives another error:

~/software/SalmonTE-master/SalmonTE.py quant --reference=m S17_R1_001.fastq.gz

[hyunhwan-jeong]

Hello @wjyzidane,

The issue seems to be related to #7, and I am wondering which version of SalmonTE you are using. If your SalmonTE version is not up-to-date then please update to the latest version. Otherwise, you can modify a part of SalmonTE.py as below:

def get_first_readid(file_name):
    with open(file_name, "r", encoding="ISO-8859-1") as inp:
        return inp.readline().split()[0]

Best Regards,

Hyun-Hwan Jeong

[hyunhwan-jeong]

The second issue, can you check the EXPR.csv has been generated and show me the list of files/directories are stored in SalmonTE_output directory?

Hyun-Hwan Jeong

[wjyzidane]

Hi Hyun-Hwan,

I fixed the first problem but for the second problem there is no EXPR file and the SalmonTE_output folder is empty.

[wjyzidane]

Btw, if I uncompress the file and run SalmonTE again, it will generate the files as below:

but still give the error as below:

Does the file generate completely?

[hyunhwan-jeong]

You must see two directories named by S17_R1_001 and S17_R2_001 in your SalmonTE_output directory if your run has been done without any problems before merging quantification result. Can you see those directories?

Also, I am suspecting you have an issue with a python package. Can you check you are having any error messages when you run below?

python3 # this should be python3
import pandas as pd # this will be executed once you are in the command line mode

Hyun-Hwan Jeong

[wjyzidane]

If I run the pair end unzip file, it gives the error as below, no SalmonTE_output folder generated. I suspect it is because the file name is not correct?

If I run the single end unzip file, it gives the error as I reported in the last post. There is SalmonTE folder with a dir called S17_R1_001 generated and files included are shown in the last post.

Looks like the "numpy" script is missing?

[hyunhwan-jeong]

@wjyzidane Oh, my bad, import pandas pd has to be import pandas as pd, and I am thinking this problem is because of the missing of numpy package, so could you reinstall numpy and pandas. If you are using pip then you can run below command lines for the reinstallation:

pip uninstall pandas
pip uninstall numpy
pip install pandas
pip install numpy

Hope this helps you.

Hyun-Hwan Jeong

[wjyzidane]

Hi Hyun-Hwan,

Thank you so much for your detailed explanation. I figured it out. I have updated my python path because I try to use some package from other people’s folder where the numpy there seems incomplete. I just delete those from my python path and everything is back to normal. Sorry for bothering you.

Best, Jingyi

在 2018年6月1日，上午1:37，Hyun-Hwan Jeong notifications@github.com 写道：

@wjyzidane https://github.com/wjyzidane Oh, my bad, import pandas pd has to be import pandas as pd, and I am thinking this problem is because of the missing of numpy package, so could you reinstall numpy and pandas. If you are using pip then you can run below command lines for the reinstallation:

pip uninstall pandas pip uninstall numpy pip install pandas pip install numpy Hope this helps you.

Hyun-Hwan Jeong

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/hyunhwaj/SalmonTE/issues/11#issuecomment-393764769, or mute the thread https://github.com/notifications/unsubscribe-auth/AhU3K9t71MhSCFaXM6_45S8H7GVxXaVxks5t4NMWgaJpZM4UVKmL.

[wjyzidane]

Btw, but I still think the name recognition is a problem for pair-end file:

[hyunhwan-jeong]

Glad to hear that, @wjyzidane !

By the way, I am wondering how you can resolve the first problem. Could you briefly explain what you did to do?

Thank you,

Hyun-Hwan Jeong

[wjyzidane]

Actually, I think there are four problems.

1 numpy package is missing. I solved it by clean the path. 2 unicode error, I solved it by modifying the script as you suggested. 3 the pair filename problem. it is unsolved as I mentioned in the last post 4 the compressed file problem. There is no error but no output as well as shown below.

I am sorry to report so many problems in one post but I just find them all at the same time.

Jingyi

[hyunhwan-jeong]

• Regarding the problem 3, could you open a new issue and explain about this?
• I am wondering which version of SalmonTE you are using. What you are able to see when you run SalmonTE.py --version?

Thank you,

Hyun-Hwan Jeong