Why the result .jsdel file of the ICRA_cmd.py for paired end data was empty?

[Cuiying20211219]

ICRA Team,

When I run the ICRA_cmd.py for paired end data, the result .jsdel file was empty.And there was no error. However, it is normal for single end data. Could you provide some guidance on how to solve this problem? Thanks!

This is the running code of paired end data : python ~/SGVFinder_211217/src/ICRA_cmd.py ./result ~/public6/cuiying/03project_public6/02CRC_SV-2021_12_19/01_fastq.file/DRR127476gap/DRR127476gap_1_kneaddata_paired --pe --debug --use_theta

This is the DEBUG information of the code :

And This is the final result: ![Uploading image.png…]()

[Cuiying20211219]

[liuronghyw]

Did you manage to solve the problem? I came across the same issue.

[treasure316]

Did you manage to solve the problem? I came across the same issue.

[treasure316]

Did you manage to solve the problem? I came across the same issue.

[talkorem]

The output above is characteristic of lack of mapping to the reference dataset. I cannot say why. We will soon publish a new repository with updated code.

[treasure316]

The output above is characteristic of lack of mapping to the reference dataset. I cannot say why. We will soon publish a new repository with updated code.

Thank you for your reply. I tried to run other queue fastq files. The.jsdel file was composed of content.But the jsdel file output of the queue I wanted to use was empty. Is it due to different queues? Or is there something wrong with kneaddata?

[treasure316]

Thank you for your reply. I tried to run other queue fastq files. The.jsdel file was composed of content.But the jsdel file output of the queue I wanted to use was empty. Is it due to different queues? Or is there something wrong with kneaddata?

[talkorem]

I do not know what you mean by queues. Try to look at the raw mappings from that specific file to see where reads map to.

[treasure316]

I do not know what you mean by queues. Try to look at the raw mappings from that specific file to see where reads map to.

Thank you for taking time out of your busy schedule to reply me.I have solved the problem. But I have another question I'd like to ask you. "https://genie.weizmann.ac.il/SV/" The website of each bacterium related website can not be opened. like this picture

[liuronghyw]

The output above is characteristic of lack of mapping to the reference dataset. I cannot say why. We will soon publish a new repository with updated code.

Thank you for your reply. I tried to run other queue fastq files. The.jsdel file was composed of content.But the jsdel file output of the queue I wanted to use was empty. Is it due to different queues? Or is there something wrong with kneaddata?

Would you please tell me how to solve this problem? Thanks!

[talkorem]

I do not know what you mean by queues. Try to look at the raw mappings from that specific file to see where reads map to.

[liuronghyw]

Did you manage to solve the problem? I came across the same issue.

Thanks for your replay. Would you please tell me how to open the file end with .pmp. I failed to open it with uedit64. Thank you very much!

[Aaron-Diao]

I do not know what you mean by queues. Try to look at the raw mappings from that specific file to see where reads map to.

Thank you for taking time out of your busy schedule to reply me.I have solved the problem. But I have another question I'd like to ask you. "https://genie.weizmann.ac.il/SV/" The website of each bacterium related website can not be opened. like this picture Friend, we meet the same question, would you please tell me how to deal with the question that the result . jsdel was empty