VAnalysis crashes: Contig::create_profile p2 SC failed

[Curtis Hendrickson (Campus)]

Dear Xiao Yang et al,

 

First, thank you for your past help with VICUNA.

 

I’ve run a lot of fastq sets through it, now, but for some reason, all the fastqs from our latest sequencing run crash in a new and interesting way:

Creating the first contig in VANALYSIS:

output to file: /scratch/user/curtish/ross/vicunaFall/SR07-05-55073-1/output//contig.0.txt

Contig::create_profile p2 SC failed

(I have attached the entire log).

I have also sent you (separately) the config.align file that VICUNA built – Dr. Yang’s Broad Inst email.

 

Any insights you can provide would be really helpful.

I’m happy to provide fastqs, reference genome, etc.

 

Regards,

Curtis

 

Research Associate, Informatics Unit

Center for Clinical and Translational Science

http://bioinformatics.uab.edu

University of Alabama at Birmingham

 

 

[HONG KAI LEE]

This happens to some of my fastq files

Rebuilding fastq files using bcl2fastq-v2.16 resolved my problem. 

https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v216-Software-Guide-15051736-E.pdf