Cannot run example files after install with mamba

[ghost]

Good afternoon. I have tried running the snakemake file after installing with mamba on a different computer (home computer). I ran the example data, and I could not get the program to execute correctly. I've attached the logs.

Thank you, snakemakelog_2.txt snakemakelog.txt

Brian

[cvn001]

Hi Brian,

Thanks for your interest in our pipeline.

From the log files you provided, we find that the software fastp and fastqc have no output files. This is most likely due to a problem with the path to the fastq file entered. Please make sure that the example data is tested in the main directory of transflow.

Xiangchen Li

[ghost]

Dr. Li.

Thank you so much for your quick response! I appreciate the advice.

I'll give it a try and let you know what happens.

Thanks,

Brian

From: Xiangchen Li @.> Sent: Tuesday, May 30, 2023 2:49 AM To: cvn001/transflow @.> Cc: Brian Delavan @.>; Author @.> Subject: Re: [cvn001/transflow] Cannot run example files after install with mamba (Issue #4)

Hi Brian,

Thanks for your interest in our pipeline.

From the log files you provided, we find that the software fastp and fastqc have no output files. This is most likely due to a problem with the path to the fastq file entered. Please make sure that the example data is tested in the main directory of transflow.

Xiangchen Li

- Reply to this email directly, view it on GitHubhttps://github.com/cvn001/transflow/issues/4#issuecomment-1567936672, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGTR2ZQ2H2Q2UGTBXC3XIWQ6TANCNFSM6AAAAAAYSDNMMY. You are receiving this because you authored the thread.Message ID: @.***>

[ghost]

HI Dr. Li.

I think I diagnosed the problem...but I don't know the solution at this time. I think the snakemake solver maybe to run a rule before the input files are present. It looks like snakemake is trying to gzip some files before the files are transferred to the temp directory.

This is a github discussion about it.

I'm not 100% sure this is what is going on, but I can't figure anything else out.

Thanks,

https://github.com/snakemake/snakemake/issues/771

@. From: Xiangchen Li @.> Sent: Tuesday, May 30, 2023 2:49 AM To: cvn001/transflow @.> Cc: Brian Delavan @.>; Author @.***> Subject: Re: [cvn001/transflow] Cannot run example files after install with mamba (Issue #4)

Hi Brian,

Thanks for your interest in our pipeline.

From the log files you provided, we find that the software fastp and fastqc have no output files. This is most likely due to a problem with the path to the fastq file entered. Please make sure that the example data is tested in the main directory of transflow.

Xiangchen Li

- Reply to this email directly, view it on GitHubhttps://github.com/cvn001/transflow/issues/4#issuecomment-1567936672, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGTR2ZQ2H2Q2UGTBXC3XIWQ6TANCNFSM6AAAAAAYSDNMMY. You are receiving this because you authored the thread.Message ID: @.***>

[ghost]

One more error on my end to consider...

@.***

From: Xiangchen Li @.> Sent: Tuesday, May 30, 2023 2:49 AM To: cvn001/transflow @.> Cc: Brian Delavan @.>; Author @.> Subject: Re: [cvn001/transflow] Cannot run example files after install with mamba (Issue #4)

Hi Brian,

Thanks for your interest in our pipeline.

From the log files you provided, we find that the software fastp and fastqc have no output files. This is most likely due to a problem with the path to the fastq file entered. Please make sure that the example data is tested in the main directory of transflow.

Xiangchen Li

- Reply to this email directly, view it on GitHubhttps://github.com/cvn001/transflow/issues/4#issuecomment-1567936672, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGTR2ZQ2H2Q2UGTBXC3XIWQ6TANCNFSM6AAAAAAYSDNMMY. You are receiving this because you authored the thread.Message ID: @.***>