The discordant_pairs file cannot be created.

km-2021

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Feb 24, 2021, 2:45:45 AM2/24/21

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Hi,

I am running JAFFA for the first time. I think I have installed everything correctly.
I am getting an error at "Stage get_unmaped".

I suggest this error is due to the discordant_pairs file not being created.

Is there a solution?

Nadia Davidson

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Feb 24, 2021, 4:14:38 AM2/24/21

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Hi,

If you are able to provide more information, I may be able to help. Some suggests of information to help us work out what's going wrong can be found at https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#other-errors

Cheers,

Nadia.

km-2021

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Mar 2, 2021, 7:15:37 PM3/2/21

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Hi,

I put reference files in JAFFA-version-1.09.

In JAFFA_stages.groovy file,

*************Path to reference files************
genome="hg38"
annotation="genCode22"

however, to use hg19, I rewrote it as follows,

genome="hg19"
annotation="genCode19".

I ran Demo data on BTB474-demo. Trimmomatic completes, but at Stage get_unmmapped, it fails with the code below.

Cannot open for reading “1.0”

Sort: cannot read: BT474-demo_discordant_pairs

When I checked the inside of the created BT474-demo folder, the BT474-demo_discordant_pairs file was not created.

2021年2月24日水曜日 18:14:38 UTC+9 nadiamd...@gmail.com:

Nadia Davidson

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Mar 3, 2021, 5:03:18 AM3/3/21

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Hi, What is output of "ls -l" run in the directory JAFFA-version-1.09?

Can you also paste the command you ran for me to double check.

Thanks,

Nadia.

km-2021

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Mar 4, 2021, 9:31:56 PM3/4/21

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Thank you for your reply,

I attached the command page.

2021年3月3日水曜日 19:03:18 UTC+9 nadiamd...@gmail.com:

Nadia Davidson

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Mar 22, 2021, 4:20:51 PM3/22/21

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Hi,

From this error message it appear that you don't have samtools installed. Once installed, you should add the path to it in the files tools.groovy in the directory where JAFFA is installed. Also check that all other paths in this file are filled incase something went wrong when you ran the installation script.