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istrope / Xenomake

Processing pipeline for Patient Derived Xenograft (PDX) Spatial Transcriptomics Datasets
https://istrope.github.io/Xenomake/
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xengsort unclassified.fq.gz missing #7

Closed ctman1025 closed 6 months ago

ctman1025 commented 6 months ago

Thank you for developing xenomake. When I analyzed the test dataset provided. The code stopped at the step of xengsort. The error is because of a missing file, i.e. unclassified.fq.gz. Does anyone encounter the same issue? I tried to increase the latency, but it didn't help. Below is the error message.

Waiting at most 5 seconds for missing files. MissingOutputException in line 99 of /home/ctman/Xenomake/snakemake/xengsort.smk: Job Missing files after 5 seconds: /home/ctman/Xenomake-out/test/xengsort/test-unclassified.fq.gz This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 14 completed successfully, but some output files are missing. 14 File "/home/ctman/miniconda3/envs/xenomake/lib/python3.10/site-packages/snakemake/executors/init.py", line 584, in handle_job_success File "/home/ctman/miniconda3/envs/xenomake/lib/python3.10/site-packages/snakemake/executors/init.py", line 252, in handle_job_success

istrope commented 6 months ago

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

ctman1025 commented 6 months ago

Hi Shawn,

Thank you for getting back to me. I would also like to ask if there is a way that we can use xenomake to analyze regular 10X scRNAseq data, which does not have spatial information. This will be very helpful for our project.

Thanks again!

Best,

Chris

From: Ivy (Shawn) Strope @.> Sent: Monday, February 19, 2024 10:57 AM To: istrope/Xenomake @.> Cc: ctman1025 @.>; Author @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

— Reply to this email directly, view it on GitHub https://github.com/istrope/Xenomake/issues/7#issuecomment-1952877989 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AM6QRC5JDWEFK5BVIMFLOR3YUN74FAVCNFSM6AAAAABDKRZMBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSHA3TOOJYHE . You are receiving this because you authored the thread. https://github.com/notifications/beacon/AM6QRC6TEBVBHBUWS774ZIDYUN74FA5CNFSM6AAAAABDKRZMBKWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTUM2G2K.gif Message ID: @. @.> >

istrope commented 6 months ago

yes, I am currently working on an update to Xenomake that will be released by the end of next week. This would extend support to 10x single-cell projects and more spatial array-based platforms.

Best, Ivy Strope

From: ctman1025 @.> Sent: Monday, February 19, 2024 11:40 AM To: istrope/Xenomake @.> Cc: Strope, Ivy Shawn @.>; Comment @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

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Hi Shawn,

Thank you for getting back to me. I would also like to ask if there is a way that we can use xenomake to analyze regular 10X scRNAseq data, which does not have spatial information. This will be very helpful for our project.

Thanks again!

Best,

Chris

From: Ivy (Shawn) Strope @.> Sent: Monday, February 19, 2024 10:57 AM To: istrope/Xenomake @.> Cc: ctman1025 @.>; Author @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

— Reply to this email directly, view it on GitHub https://github.com/istrope/Xenomake/issues/7#issuecomment-1952877989 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AM6QRC5JDWEFK5BVIMFLOR3YUN74FAVCNFSM6AAAAABDKRZMBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSHA3TOOJYHE . You are receiving this because you authored the thread. https://github.com/notifications/beacon/AM6QRC6TEBVBHBUWS774ZIDYUN74FA5CNFSM6AAAAABDKRZMBKWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTUM2G2K.gif Message ID: @. @.> >

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ctman1025 commented 6 months ago

Hi Ivy,

This is awesome. Thank you for your work for the community. If you have an early version with regular 10X scRNAseq capability, I would like to give a try on our data and perhaps give you some feedback.

Please let me know.

Best,

Chris

From: Ivy Shawn Strope @.> Sent: Monday, February 19, 2024 12:10 PM To: istrope/Xenomake @.> Cc: ctman1025 @.>; Author @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

yes, I am currently working on an update to Xenomake that will be released by the end of next week. This would extend support to 10x single-cell projects and more spatial array-based platforms.

Best, Ivy Strope

From: ctman1025 @. <mailto:@.> > Sent: Monday, February 19, 2024 11:40 AM To: istrope/Xenomake @. <mailto:@.> > Cc: Strope, Ivy Shawn @. <mailto:@.> >; Comment @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

CAUTION: This email is not from a BCM Source. Only click links or open attachments you know are safe.

Hi Shawn,

Thank you for getting back to me. I would also like to ask if there is a way that we can use xenomake to analyze regular 10X scRNAseq data, which does not have spatial information. This will be very helpful for our project.

Thanks again!

Best,

Chris

From: Ivy (Shawn) Strope @. <mailto:@.> > Sent: Monday, February 19, 2024 10:57 AM To: istrope/Xenomake @. <mailto:@.> > Cc: ctman1025 @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

— Reply to this email directly, view it on GitHub https://github.com/istrope/Xenomake/issues/7#issuecomment-1952877989 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AM6QRC5JDWEFK5BVIMFLOR3YUN74FAVCNFSM6AAAAABDKRZMBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSHA3TOOJYHE . You are receiving this because you authored the thread. https://github.com/notifications/beacon/AM6QRC6TEBVBHBUWS774ZIDYUN74FA5CNFSM6AAAAABDKRZMBKWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTUM2G2K.gif Message ID: @. <mailto:@.> @. <mailto:@.> > >

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istrope commented 6 months ago

I will let you know when I have an updated branch on Github ready for testing. Having someone to help find bugs would be wonderful. Thank you very much

Best, Ivy

From: ctman1025 @.> Sent: Monday, February 19, 2024 1:30 PM To: istrope/Xenomake @.> Cc: Strope, Ivy Shawn @.>; Comment @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

Hi Ivy,

This is awesome. Thank you for your work for the community. If you have an early version with regular 10X scRNAseq capability, I would like to give a try on our data and perhaps give you some feedback.

Please let me know.

Best,

Chris

From: Ivy Shawn Strope @.> Sent: Monday, February 19, 2024 12:10 PM To: istrope/Xenomake @.> Cc: ctman1025 @.>; Author @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

yes, I am currently working on an update to Xenomake that will be released by the end of next week. This would extend support to 10x single-cell projects and more spatial array-based platforms.

Best, Ivy Strope

From: ctman1025 @. <mailto:@.> > Sent: Monday, February 19, 2024 11:40 AM To: istrope/Xenomake @. <mailto:@.> > Cc: Strope, Ivy Shawn @. <mailto:@.> >; Comment @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

CAUTION: This email is not from a BCM Source. Only click links or open attachments you know are safe.

Hi Shawn,

Thank you for getting back to me. I would also like to ask if there is a way that we can use xenomake to analyze regular 10X scRNAseq data, which does not have spatial information. This will be very helpful for our project.

Thanks again!

Best,

Chris

From: Ivy (Shawn) Strope @. <mailto:@.> > Sent: Monday, February 19, 2024 10:57 AM To: istrope/Xenomake @. <mailto:@.> > Cc: ctman1025 @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

— Reply to this email directly, view it on GitHub https://github.com/istrope/Xenomake/issues/7#issuecomment-1952877989 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AM6QRC5JDWEFK5BVIMFLOR3YUN74FAVCNFSM6AAAAABDKRZMBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSHA3TOOJYHE . You are receiving this because you authored the thread. https://github.com/notifications/beacon/AM6QRC6TEBVBHBUWS774ZIDYUN74FA5CNFSM6AAAAABDKRZMBKWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTUM2G2K.gif Message ID: @. <mailto:@.> @. <mailto:@.> > >

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ctman1025 commented 6 months ago

You bet. Thank you! Please keep me posted. Have a nice day!

From: Ivy Shawn Strope @.> Sent: Monday, February 19, 2024 1:50 PM To: istrope/Xenomake @.> Cc: ctman1025 @.>; Author @.> Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

I will let you know when I have an updated branch on Github ready for testing. Having someone to help find bugs would be wonderful. Thank you very much

Best, Ivy

From: ctman1025 @. <mailto:@.> > Sent: Monday, February 19, 2024 1:30 PM To: istrope/Xenomake @. <mailto:@.> > Cc: Strope, Ivy Shawn @. <mailto:@.> >; Comment @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

Hi Ivy,

This is awesome. Thank you for your work for the community. If you have an early version with regular 10X scRNAseq capability, I would like to give a try on our data and perhaps give you some feedback.

Please let me know.

Best,

Chris

From: Ivy Shawn Strope @. <mailto:@.> > Sent: Monday, February 19, 2024 12:10 PM To: istrope/Xenomake @. <mailto:@.> > Cc: ctman1025 @. <mailto:@.> >; Author @. <mailto:@.> > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

yes, I am currently working on an update to Xenomake that will be released by the end of next week. This would extend support to 10x single-cell projects and more spatial array-based platforms.

Best, Ivy Strope

From: ctman1025 @. <mailto:@.> mailto:***@***.*** > Sent: Monday, February 19, 2024 11:40 AM To: istrope/Xenomake @. <mailto:@.> mailto:***@***.*** > Cc: Strope, Ivy Shawn @. <mailto:@.> mailto:***@***.*** >; Comment @. <mailto:@.> mailto:***@***.*** > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

CAUTION: This email is not from a BCM Source. Only click links or open attachments you know are safe.

Hi Shawn,

Thank you for getting back to me. I would also like to ask if there is a way that we can use xenomake to analyze regular 10X scRNAseq data, which does not have spatial information. This will be very helpful for our project.

Thanks again!

Best,

Chris

From: Ivy (Shawn) Strope @. <mailto:@.> mailto:***@***.*** > Sent: Monday, February 19, 2024 10:57 AM To: istrope/Xenomake @. <mailto:@.> mailto:***@***.*** > Cc: ctman1025 @. <mailto:@.> mailto:***@***.*** >; Author @. <mailto:@.> mailto:***@***.*** > Subject: Re: [istrope/Xenomake] xengsort unclassified.fq.gz missing (Issue #7)

thank you for bringing this to my attention, I have updated the file called snakemake/xengsort.smk to fix this problem.

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