search

bcgsc / NanoSim

Nanopore sequence read simulator
Other
217 stars 51 forks source link

Bug: fastq sequence and quality length different #98

Closed myhsi closed 3 years ago

myhsi commented 3 years ago

Hi, I generated some fastq reads using one of your models but it generates files which occasionally contain sequences where the sequence length and the quality length in the fastq file are different. This came up because I was trying to characterize the data with Nanoplot and it threw an error message:

ValueError: Lengths of sequence and quality values differs for NC-003210_732235_aligned_1432_F_2089_47_1342 (3478 and 3518). """

kmnip commented 3 years ago

Hi @myhsi ,

We are aware of the bug. It was fixed in commit 039ecd6 .

Ka Ming

myhsi commented 3 years ago

@kmnip, was this pushed to the latest conda package? I encountered the issue while using v2.6.0 installed through conda. Thanks!

kmnip commented 3 years ago

No, it isn't because the bug was discovered and fixed after v2.6.0 was released. We are finalising some changes for a new release soon.

eppinglen commented 3 years ago

Hi, I am getting the same error while simulating metagenome reads with version 3.0. Lengths of sequence and quality values differs for NZ-CP031256_4650403;aligned_0_F_17_12723_2 (12753 and 30461).

SaberHQ commented 3 years ago

@cheny19 it seems like that @eppinglen has the same issue with the version 3.0 as well. I am reopening the issue.

cheny19 commented 3 years ago

@eppinglen @SaberHQ ,

Thanks for reporting this. It's a different bug than the previous one and this only exists in the metagenome simulation. I have fixed this and officially made release 3.0.0. Please let me know if there's any further questions.

Cheers, Chen

eppinglen commented 3 years ago

@cheny19 Thank you for the quick response. It is working fine now.