Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Break10x runtime error - missing file #2

Open
JordideRaad opened this issue Jun 1, 2018 · 0 comments
Open

Break10x runtime error - missing file #2

JordideRaad opened this issue Jun 1, 2018 · 0 comments

Comments

@JordideRaad
Copy link

Dear Francesca Giordano,

I am currently trying to optimize my 10x chromium de-novo assembly and am trying out different tools to check for assembly errors. The Scaff10x function seems to work perfectly. However, if I try to run the Break10x, I get the following error:

...
[M::mem_pestat] low and high boundaries for proper pairs: (1, 823)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 1535158 reads in 519.780 CPU sec, 20.325 real sec
[main] Version: 0.7.17-r1194-dirty
[main] CMD: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/bwa mem -t 30 tarseq.fastq /home/user/my_data/N15_10x/raw_reads/read-BC_1.fastq /home/jderaad/my_data/N15_10x/raw_reads/read-BC_2.fastq
[main] Real time: 234729.355 sec; CPU: 201340.607 sec
sh: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/scaff_barcode-length: No such file or directory
sort: cannot read: align.length-5: No such file or directory

There appears to be an error due to the missing "scaff_barcode-length" file and there is no file named "scaff_barcode-length" in the softwares/scaff10x/Scaff10X/src/scaff-bin directory. Is this an error in the script or am I missing a crucial file?

Kind regards,

Jordi

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant