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Failed to open file output.bam #10

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yuanqm55 opened this issue Sep 11, 2018 · 8 comments
Open

Failed to open file output.bam #10

yuanqm55 opened this issue Sep 11, 2018 · 8 comments

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@yuanqm55
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I follow the instructions(install dependencies, set paths, download data and index the reference sequence), and everything's going well. Then I run run_vifi.py using the test data(test_R1.fq.gz and test_R2.fq.gz) and ran into a problem: Failed to open file output.bam.
helpme
@namphuon
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namphuon commented Sep 11, 2018 via email

@yuanqm55
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Can you let me know what's in the folder ./test_result? I am wondering if it might be some path issue. I don't know if this would impact it, but maybe try giving the full path to the -o option. If that does work, I'll fix my code so that full path is not needed.
…
On Tue, Sep 11, 2018 at 2:06 AM, 阿克苏地 @.***> wrote: I follow the instructions(install dependencies, set paths, download data and index the reference sequence), and everything's going well. Then I run run_vifi.py using the test data(test_R1.fq.gz and test_R2.fq.gz) and ran into a problem: Failed to open file output.bam. [image: helpme] https://user-images.githubusercontent.com/34777741/45349803-dd040800-b5e4-11e8-8490-0de1ecaab050.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10>, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5tNMnz20mY5FbqTb4a-0U87WSI7l77ks5uZ3z7gaJpZM4Wi5HR .
-- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0404

Here's the items in the folder ./test_result:
what s in
And the program seems to work after I gave the full path to the -o option, as you suggested.
However, I run into a new issue:TypeError: AlignmentHeader does not support item assignment (use header.to_dict()
newproblem
I'm a newcomer to bioinformatics. Thanks for helping!

@namphuon
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namphuon commented Sep 24, 2018 via email

@yuanqm55
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Hi, I believe this issue was due to ViFi not being compatible with the latest version of pysam. I've updated the code. Can you try the latest version and let me know if you still have an issue? Thanks! Regards, Nam
…
On Sun, Sep 16, 2018 at 10:04 PM, 阿克苏地 @.> wrote: Can you let me know what's in the folder ./test_result? I am wondering if it might be some path issue. I don't know if this would impact it, but maybe try giving the full path to the -o option. If that does work, I'll fix my code so that full path is not needed. … <#m_1651321738927992081_> On Tue, Sep 11, 2018 at 2:06 AM, 阿克苏地 @.> wrote: I follow the instructions(install dependencies, set paths, download data and index the reference sequence), and everything's going well. Then I run run_vifi.py using the test data(test_R1.fq.gz and test_R2.fq.gz) and ran into a problem: Failed to open file output.bam. [image: helpme] https://user-images.githubusercontent.com/34777741/45349803-dd040800- b5e4-11e8-8490-0de1ecaab050.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #10 <#10>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5tNMnz20mY5FbqTb4a- 0U87WSI7l77ks5uZ3z7gaJpZM4Wi5HR . -- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093 https://maps.google.com/?q=9500+Gilman+Drive,+La+Jolla,+CA+92093&entry=gmail&source=g -0404 Here's the items in the folder ./test_result: [image: what s in] https://user-images.githubusercontent.com/34777741/45605761-1bc91080-ba72-11e8-8f3e-4966cf37d879.png And the program seems to work after I gave the full path to the -o option, as you suggested. However, I run into a new issue:TypeError: AlignmentHeader does not support item assignment (use header.to_dict() [image: newproblem] https://user-images.githubusercontent.com/34777741/45606533-736a7a80-ba78-11e8-8fed-dd141a53b623.png I'm a newcomer to bioinformatics. Thanks for helping! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5tND86dvZIGOiqI6rDNw9ZIzDsb8jPks5uby1wgaJpZM4Wi5HR .
-- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0404

Hi,
After I tried the latest version, pysam seemed to work normally.
1

However, the program stalled here for over 2 hours when running the test data:
2

and finally the program seemed to killed itself.
kill2

Note that output.clusters.txt and output.clusters.txt.range is empty.
In addition, when the program stalled, memory was uesed 99%.
default

Thanks for helping!

@namphuon
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namphuon commented Sep 27, 2018 via email

@yuanqm55
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Thanks for the summary. Is it correct that you have 16 GB of RAM on your machine? I will look into what caused the issue and will get back to you. Regards, Nam
…
On Thu, Sep 27, 2018 at 7:34 AM, 阿克苏地 @.> wrote: Hi, I believe this issue was due to ViFi not being compatible with the latest version of pysam. I've updated the code. Can you try the latest version and let me know if you still have an issue? Thanks! Regards, Nam … <#m_-3372050740237915504_> On Sun, Sep 16, 2018 at 10:04 PM, 阿克苏地 @.> wrote: Can you let me know what's in the folder ./test_result? I am wondering if it might be some path issue. I don't know if this would impact it, but maybe try giving the full path to the -o option. If that does work, I'll fix my code so that full path is not needed. … <#m_1651321738927992081_> On Tue, Sep 11, 2018 at 2:06 AM, 阿克苏地 @.***> wrote: I follow the instructions(install dependencies, set paths, download data and index the reference sequence), and everything's going well. Then I run run_vifi.py using the test data(test_R1.fq.gz and test_R2.fq.gz) and ran into a problem: Failed to open file output.bam. [image: helpme] https://user-images. githubusercontent.com/34777741/45349803-dd040800- b5e4-11e8-8490-0de1ecaab050.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < #10 <#10> <#10 <#10>>>, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5tNMnz20mY5FbqTb4a- 0U87WSI7l77ks5uZ3z7gaJpZM4Wi5HR . -- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093 https://maps.google.com/?q=9500+Gilman+Drive,+La+Jolla,+CA+92093&entry=gmail&source=g https://maps.google.com/?q=9500+Gilman+Drive,+La+Jolla,+ CA+92093&entry=gmail&source=g -0404 Here's the items in the folder ./test_result: [image: what s in] https://user-images. githubusercontent.com/34777741/45605761-1bc91080- ba72-11e8-8f3e-4966cf37d879.png And the program seems to work after I gave the full path to the -o option, as you suggested. However, I run into a new issue:TypeError: AlignmentHeader does not support item assignment (use header.to_dict() [image: newproblem] https://user-images. githubusercontent.com/34777741/45606533-736a7a80- ba78-11e8-8fed-dd141a53b623.png I'm a newcomer to bioinformatics. Thanks for helping! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment) <#10 (comment)>>, or mute the thread https://github.com/notifications/unsubscribe-auth/ AA5tND86dvZIGOiqI6rDNw9ZIzDsb8jPks5uby1wgaJpZM4Wi5HR . -- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093 https://maps.google.com/?q=9500+Gilman+Drive,+La+Jolla,+CA+92093&entry=gmail&source=g -0404 Hi, After I tried the latest version, pysam seemed to work normally. [image: 1] https://user-images.githubusercontent.com/34777741/46153070-012e3d00-c2a5-11e8-97e7-ccdb51e94c33.png However, the program stalled here for over 2 hours when running the test data: [image: 2] https://user-images.githubusercontent.com/34777741/46153064-fb385c00-c2a4-11e8-8a34-2516f4c3c9fd.png and finally the program seemed to killed itself. [image: kill2] https://user-images.githubusercontent.com/34777741/46153048-f4114e00-c2a4-11e8-920e-28144d07510c.png Note that output.clusters.txt and output.clusters.txt.range is empty. In addition, when the program stalled, memory was uesed 99%. [image: default] https://user-images.githubusercontent.com/34777741/46153036-e8258c00-c2a4-11e8-9de7-94f389902801.png Thanks for helping! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AA5tNJIc6gQL_dNerTfZ41Z5F-3j72ujks5ufOHkgaJpZM4Wi5HR .
-- Nam-phuong Nguyen, PhD Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0404

Hi, it is correct that I have 16 GB of RAM on my machine. Thanks in advance :)

@namphuon
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namphuon commented Oct 15, 2018 via email

@ibqcarlos
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Hi Nam,
I have a similar problem and I think it's with the cluster_trans_new.py script. I attach some images of the problem.
captura de pantalla de 2018-11-07 19-18-53
captura de pantalla de 2018-11-07 19-25-56

Thank you,
Carlos

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@namphuon @yuanqm55 @ibqcarlos