Frozen at 91%

[acuadros1]

I have been trying for the past 2 days to troubleshoot an issue with the analysis tool. It is constantly stuck at 91% and "generating Fastq quality report" for several hours.
I uploaded a cutom Fasta file for a subpool library made. The format for the entries are genename_seq (i.e. Tim20_GACCATCGTGACTGGATCGT) so I input the custom regular expression: ^(.+?)_(.*)$
My raw data was uploaded as fastq.gz compressed files. The vector used was a lentiguide Puro and all my sequences have the "CACCG-20nt sgRNA-GTTTT" motif. Since the default LGPuro regular expressions are ACC(.{20,21})G I have used a custom expression: ACCG(.{20})G
Still the program hangs at 91% for several hours. Any fixes for this you have experienced? Thanks in advance.

[jwinter6]

Hi,
could you drop me some fasta/fastq files (or parts of it)?

Best,
Jan

[acuadros1]

Hi Jan, I have it working now I just started from read counts instead. Best, Alex Cuadros On 21 May 2020, at 17:15, Jan Winter <[email protected]> wrote:  Hi, could you drop me some fasta/fastq files (or parts of it)? Best, Jan — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#62 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APTOBY6OCHG4CN2TVDKBFGLRSVAOTANCNFSM4NDDEZ4Q>. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#62 (comment)", "url": "#62 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[afaissa]

Hi,

Thanks for the package, but I have the same problem here. Using four fastq files (~1GB each) didn´t pass the first step. If I upload only two, it works on the first step but it stops on 9% on the the "Check Gene and sgRNA Readcount for consistency".

It is running for 4 hours and there is no error message, though.

Best,