Thanks for developing this great tool. I am trying to use your program to remove primers from MiSeq library. My inserts are DNA of different length, over a range of ~320 to 390 nt. With Ubuntu 20.04.1 LTS, I encountered “ buffer overflow detected” problem and program was terminated almost immediately, with about 100,000 reads processed in less than one second. One of my fastq files contains ~3 million reads, another only 300,000 reads. They both had this buffer overflow problem. When I put the first 100 reads into a separate file, you program handle it perfectly. I tested your example files and it worked well too.
Could you help to figure out what might be the cause of this? I know you worked on 11 million reads in your paper in 27 seconds, back to 2017. Maybe it is a problem introduced in you latest update?
By the way, my inserts are about 320-390nt long (peak at around 360 nt) amplified with a single primer pair. In the primer info file, I set a value of 340 for insert length. I notice that your program will covert any reads with insert less than 340 nt into NNNNNN..... After I changed the insert length to 300 in the primer file, all reads are properly trimmed. Interesting.
This is a great tool and thank you so much for developing it.
Hi Xiaolong,
Thanks for developing this great tool. I am trying to use your program to remove primers from MiSeq library. My inserts are DNA of different length, over a range of ~320 to 390 nt. With Ubuntu 20.04.1 LTS, I encountered “ buffer overflow detected” problem and program was terminated almost immediately, with about 100,000 reads processed in less than one second. One of my fastq files contains ~3 million reads, another only 300,000 reads. They both had this buffer overflow problem. When I put the first 100 reads into a separate file, you program handle it perfectly. I tested your example files and it worked well too.
Could you help to figure out what might be the cause of this? I know you worked on 11 million reads in your paper in 27 seconds, back to 2017. Maybe it is a problem introduced in you latest update?
By the way, my inserts are about 320-390nt long (peak at around 360 nt) amplified with a single primer pair. In the primer info file, I set a value of 340 for insert length. I notice that your program will covert any reads with insert less than 340 nt into NNNNNN..... After I changed the insert length to 300 in the primer file, all reads are properly trimmed. Interesting.
This is a great tool and thank you so much for developing it.
Jianliang