Re: from Molkentin Lab, CCHMC: regd. AtlAnalyze analysis pipeline.

[AltAnalyze CCHMC]

Hi Vikram,

The first thing I see is that the software is very old. I recommend downloading the latest version from the website and running. How many BAM files is this?

Best,

Nathan

On Jun 21, 2021, at 12:38 PM, Prasad, Vikram <Vikram...@cchmc.org> wrote:



Good Afternoon,

 

We are attempting to use the AltAnalyze software to run our RNAseq analysis pipeline and repeatedly run into a problem, where the program stalls with an error message (pl. see attached image).

 

The BAM files for this analysis were generated at the CCHMC DNA Core, where sequencing was done PE/40M.

 

I would appreciate it if you could provide suggestions/advice on how this error might be rectified or worked around (the log file is also attached).

 

Thanking you in advance for your time and effort,

 

Vikram Prasad

<AltAnalyze_report-20210621-100603.log>

<AltAnalyze_error-message.jpeg>

[Prasad, Vikram]

[Prasad, Vikram]

Hi Nathan,

 

The project currently includes 8 BAM files. It will expand to 16 in the weeks ahead.

 

I will download a more recent version of the software as you suggest.

 

Thanks,

Vikram

 

From: AltAnalyze CCHMC <altan...@gmail.com>
Sent: Monday, June 21, 2021 12:44 PM
To: Prasad, Vikram <Vikram...@cchmc.org>
Cc: gen...@gladstone.ucsf.edu; alt_pre...@googlegroups.com
Subject: Re: from Molkentin Lab, CCHMC: regd. AtlAnalyze analysis pipeline.

 

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[Nathan Salomonis]

Great,

That should be fine. For dozens of BAM files I recommend running certain steps in parallel on the cluster, but 8-16 should be fine, but the pre-processing steps can take a while when run in the default single-processor mode (which is used to minimize process conflicts). Let me know if you see any other errors. It is possible that the BAM files from the sequencing core are missing some standard BAM fields, which would require re-alignment from the FASTQ files with STAR (let us know if this is the case).

Best,

Nathan

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