visualize results problem

[pb-max]

I submited my fa-file in PhaBOX2 ,
everything is OK
But the visualization is no reaction, and there is no pictures
Thank you for addressing it!
Anyone have this problem?

[KennthShang]

Hi @pb-max ,

If you refer to the jobs on our webserver, please email me your jobID for further assistance. jiayushang@cuhk.edu.hk Thanks.

Best,
Jiayu

[pb-max]

My job ID is PhaBOX-20250402-UI0XZKCOU3 Thank you ! 裴冰 ***@***.***  

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------------------ 原始邮件 ------------------ 发件人: "KennthShang/PhaBOX" ***@***.***>; 发送时间: 2025年4月2日(星期三) 下午5:30 ***@***.***>; ***@***.******@***.***>; 主题: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Hi @pb-max , If you refer to the jobs on our webserver, please email me your jobID for further assistance. ***@***.*** Thanks. Best, Jiayu — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***> KennthShang left a comment (KennthShang/PhaBOX#64) Hi @pb-max , If you refer to the jobs on our webserver, please email me your jobID for further assistance. ***@***.*** Thanks. Best, Jiayu — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KennthShang]

Hi @pb-max

It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC

Best,
Jiayu

[pb-max]

Thank you very much! The result is perfect. Is it my data problem or the server problem? This is the first time for me to use this tool and I don't know much about it

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________________________________ From: ***@***.*** ***@***.***> on behalf of SHANG Jiayu ***@***.***> Sent: Wednesday, April 2, 2025 11:43 AM To: KennthShang/PhaBOX ***@***.***> Cc: pb-max ***@***.***>; Mention ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***> [KennthShang]KennthShang left a comment (KennthShang/PhaBOX#64)<#64 (comment)> Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[pb-max]

I checked the results. I submitted 35 sequences, my job PhaBOX-20250402-UI0XZKCOU3 result is still 35 This job PhaBOX-20250402-3VGLE603ZC is 23. Phamer_prediction.tsv shows that 12 non-virus

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________________________________ From: ***@***.*** ***@***.***> Sent: Wednesday, April 2, 2025 11:50 AM To: KennthShang/PhaBOX ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Thank you very much! The result is perfect. Is it my data problem or the server problem? This is the first time for me to use this tool and I don't know much about it

________________________________ From: ***@***.*** ***@***.***> on behalf of SHANG Jiayu ***@***.***> Sent: Wednesday, April 2, 2025 11:43 AM To: KennthShang/PhaBOX ***@***.***> Cc: pb-max ***@***.***>; Mention ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***> [KennthShang]KennthShang left a comment (KennthShang/PhaBOX#64)<#64 (comment)> Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KennthShang]

@pb-max , only 23 is shown in the results because I only submit the "virus" as input to the phabox.

The problem is probably caused by the system, not your problem. But we did not figure out why, since we re-submitted your inputs again, and it worked.

You can also install the local version under this github to run large-scale data and avoid potential problems caused by the server.

Best,
Jiayu

[pb-max]

I also rerun it. It seems result different from yours and my first. The visualization is ok. The results are different

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________________________________ From: ***@***.*** ***@***.***> Sent: Wednesday, April 2, 2025 12:12 PM To: KennthShang/PhaBOX ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) I checked the results. I submitted 35 sequences, my job PhaBOX-20250402-UI0XZKCOU3 result is still 35 This job PhaBOX-20250402-3VGLE603ZC is 23. Phamer_prediction.tsv shows that 12 non-virus

________________________________ From: ***@***.*** ***@***.***> Sent: Wednesday, April 2, 2025 11:50 AM To: KennthShang/PhaBOX ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Thank you very much! The result is perfect. Is it my data problem or the server problem? This is the first time for me to use this tool and I don't know much about it

________________________________ From: ***@***.*** ***@***.***> on behalf of SHANG Jiayu ***@***.***> Sent: Wednesday, April 2, 2025 11:43 AM To: KennthShang/PhaBOX ***@***.***> Cc: pb-max ***@***.***>; Mention ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***> [KennthShang]KennthShang left a comment (KennthShang/PhaBOX#64)<#64 (comment)> Hi @pb-max<https://github.com/pb-max> It seems there are "read and write errors" in the file system, and I have rerun your task. You can check the results via: PhaBOX-20250402-3VGLE603ZC Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LAZZ6QHDNZAZGCHGVD2XPEOVAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGI4TOOBZHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KennthShang]

PhaBOX-20250402-3VGLE603ZC is the one that uses an intermediate output of PhaBOX-20250402-UI0XZKCOU3

and

PhaBOX-20250402-KWGPAEL18E is my rerun, one that uses the original inputs of PhaBOX-20250402-UI0XZKCOU3. I also found the difference. 27 virus vs. 8 non-virus.

So I think this might because when the server was running the PhaBOX-20250402-UI0XZKCOU3, the file system error occurs and lead to a wrong intermediate output with error. Maybe rerunning the task at the every beginning will be the best choice if the problems happened :)

Best,
Jiayu

[pb-max]

27 virus vs. 8 non-virus. I got the same result the second time But I have another question: I think the input sequences are virus , identified by virsorter2. Why does the result have non-virus? Thank you

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________________________________ From: ***@***.*** ***@***.***> on behalf of SHANG Jiayu ***@***.***> Sent: Wednesday, April 2, 2025 1:27 PM To: KennthShang/PhaBOX ***@***.***> Cc: pb-max ***@***.***>; Mention ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) PhaBOX-20250402-3VGLE603ZC is the one that uses an intermediate output of PhaBOX-20250402-UI0XZKCOU3 and PhaBOX-20250402-KWGPAEL18E is my rerun, one that uses the original inputs of PhaBOX-20250402-UI0XZKCOU3. I also found the difference. 27 virus vs. 8 non-virus. So I think this might because when the server was running the PhaBOX-20250402-UI0XZKCOU3, the file system error occurs and lead to a wrong intermediate output with error. Maybe rerunning the task at the every beginning will be the best choice if the problems happened :) Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LHY6LRG3XFVD3ZSVAD2XPQTHAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGU3DINZVGM>. You are receiving this because you were mentioned.Message ID: ***@***.***> [KennthShang]KennthShang left a comment (KennthShang/PhaBOX#64)<#64 (comment)> PhaBOX-20250402-3VGLE603ZC is the one that uses an intermediate output of PhaBOX-20250402-UI0XZKCOU3 and PhaBOX-20250402-KWGPAEL18E is my rerun, one that uses the original inputs of PhaBOX-20250402-UI0XZKCOU3. I also found the difference. 27 virus vs. 8 non-virus. So I think this might because when the server was running the PhaBOX-20250402-UI0XZKCOU3, the file system error occurs and lead to a wrong intermediate output with error. Maybe rerunning the task at the every beginning will be the best choice if the problems happened :) Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LHY6LRG3XFVD3ZSVAD2XPQTHAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGU3DINZVGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KennthShang]

No tool has a 100% accuracy, so the results from VirSorter2 can contain false positives as indicated in their guidelines (phaboxs either).

For those identified as non-virus, you can also check their contamination using phabox2 and decide whether they should be used in the downstream analysis (run seperate task in phabox2).

Best,
Jiayu

[pb-max]

I have used CheckV to assess the sequence before. The levels of contamination identified by PhaBOX2 as non-virus ranged from high to low, some are even zero. No tool has a 100% accuracy, it is common in metagenomic analysis. Thank you very much for your patient answer, and the software you developed is expedient!

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________________________________ From: ***@***.*** ***@***.***> on behalf of SHANG Jiayu ***@***.***> Sent: Wednesday, April 2, 2025 1:52 PM To: KennthShang/PhaBOX ***@***.***> Cc: pb-max ***@***.***>; Mention ***@***.***> Subject: Re: [KennthShang/PhaBOX] visualize results problem (Issue #64) No tool has a 100% accuracy, so the results from VirSorter2 can contain false positives as indicated in their guidelines (phaboxs either). For those identified as non-virus, you can also check their contamination using phabox2 and decide whether they should be used in the downstream analysis (run seperate task in phabox2). Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LFXFEMTC6GHKOOBPET2XPTQHAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGYZTKMBVGM>. You are receiving this because you were mentioned.Message ID: ***@***.***> [KennthShang]KennthShang left a comment (KennthShang/PhaBOX#64)<#64 (comment)> No tool has a 100% accuracy, so the results from VirSorter2 can contain false positives as indicated in their guidelines (phaboxs either). For those identified as non-virus, you can also check their contamination using phabox2 and decide whether they should be used in the downstream analysis (run seperate task in phabox2). Best, Jiayu — Reply to this email directly, view it on GitHub<#64 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASQP4LFXFEMTC6GHKOOBPET2XPTQHAVCNFSM6AAAAAB2I3ZZV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONZSGYZTKMBVGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KennthShang]

Good to know. Then, you should use those contigs with low/zero contamination for downstream analysis.

Also, thanks for using our tools.

Best,
Jiayu