Exiting because a job execution failed.

[morispi]

Hello,

Sorry to bother you again.
I'm attempting to run Novel-X on the following 10x Genomics bam file : ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/10XGenomics/ , and on the associated reference genome.

However, after running for a while, Novel-X stops and indicates a job execution failed. Please find the log file attached here:
log.txt

I can see two warning messages:

• One indicates that I seem to be using an obsolete version of Blast+ and that I should try to user a newer version. However, I don't have root access on the cluster Novel-X is running, and cannot update it myself.

• The other indicates that @rg tags are missing in the BAM file. Complete warning message is here:

WARNING: no @RG (read group) headers found in BAM file. Splitting data by the GEM group marked in the corrected barcode tag.
Reads without a corrected barcode will not appear in output FASTQs
Unrecognized 10x BAM file. For BAM files produced by older pipelines, use one of the following flags:
--gemcode   BAM files created with GemCode data using Longranger 1.0 - 1.3
--lr20      BAM files created with Longranger 2.0 using Chromium Genome data
--cr11      BAM files created with Cell Ranger 1.0-1.1 using Single Cell 3' v1 data

Do you have any idea what could be causing this issue? I'm not sure which command is associated to the "no @rg" warning, so I could not attempt to tweak it myself by adding --gemcode, --lr20, or --cr11 to see if it would work.

Thanks in advance for your help.

Best,
Pierre

edit: Forgot to mention, but I'm running on a node with 150 GB of RAM, so memory should not be a problem.

[1dayac]

Hello Pierre,
Sorry, I received this message during vacation. I will look at it closely this week

[1dayac]

Apart from this issue, I don't recommend using Novel-X on this dataset. The specification says that it is round 20X (3 times lower than the usual coverage), and Novel-X is not supposed to work. For NA24385 dataset I used data from https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=HG002/hpp_HG002_NA24385_son_v1/10XG/giab_chromium_data/10XGenomics_ChromiumGenome_LongRanger2.2_Supernova2.0.1_04122018_high_coverage_bams/ (https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0/blob/master/README.md).
But I still planning to look into the issue itself

[maggs-x]

Hi, it's been a few years since this thread, does Novel-X still not work on lower coverage datasets? What's the minimum coverage you'd suggest?

Maggs

[1dayac]

Unfortunately not... I would suggest to start from at least 30X, but results will saturate at around 50X пн, 2 окт. 2023 г. в 18:10, maggs-x ***@***.***>:

…

Hi, it's been a few years since this thread, does Novel-X still not work on lower coverage datasets? What's the minimum coverage you'd suggest? Maggs — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKP3LOFJQLBJBWFYF52MKLX5LKO5AVCNFSM4SQIZ5NKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZUGMZDAMRQG4YA> . You are receiving this because you commented.Message ID: ***@***.***>

[maggs-x]

Awesome thanks so much! Maggs X they/them

________________________________ From: Dmitry Meleshko ***@***.***> Sent: Monday, October 2, 2023 12:33:36 PM To: 1dayac/Novel-X ***@***.***> Cc: maggs-x ***@***.***>; Comment ***@***.***> Subject: Re: [1dayac/Novel-X] Exiting because a job execution failed. (#3) Unfortunately not... I would suggest to start from at least 30X, but results will saturate at around 50X пн, 2 окт. 2023 г. в 18:10, maggs-x ***@***.***>:

Hi, it's been a few years since this thread, does Novel-X still not work on lower coverage datasets? What's the minimum coverage you'd suggest? Maggs — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKP3LOFJQLBJBWFYF52MKLX5LKO5AVCNFSM4SQIZ5NKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZUGMZDAMRQG4YA> . You are receiving this because you commented.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub<#3 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7HSYLWUI5S2X7J2VZEOC5TX5L3HBAVCNFSM4SQIZ5NKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZUGM2DKNRVG4ZA>. You are receiving this because you commented.Message ID: ***@***.***>