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DMU-lilab / pTrimmer

Used to trim off the primer sequence from mutiplex amplicon sequencing
GNU General Public License v3.0
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Error message #27

Open vera-rykalina opened 1 month ago

vera-rykalina commented 1 month ago

Hi,

I am just testing the tool on my FASTQ files and always getting an error "buffer overflow detected". What does it mean?

Do FASTQ files need any preprocessing (e.g. a header change)?

Should the tool also work when there are only four overlapping regions with long insertion sizes, e.g. like here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502977/

Thanks in advance.

XLZH commented 1 month ago

@vera-rykalina could you please provide a small subset of reads to reproduce the error? For the example you mentioned above, I never test it before, but I think it can work well if the primer-pair is given

vera-rykalina commented 1 month ago

Thanks for your quick reply. I will do it on Monday when I am the institute. By the way, I installed the tool on HPC via conda which is supposed to give me version 1.4.0. The installed version is 1.3.3 although according to the help message.

XLZH commented 1 month ago

The conda package is not maintained by our group, therefore, it is not updated now. I advise you download the v1.4.0 here and install it according to the INSTALL, because I have refactored the part of handling FASTQ reads.

vera-rykalina commented 1 month ago

I believe, it was an outdated version of the SW that caused the issue. I could get all the output files, using version 1.4.0. However, all reads in the output files contain only N's.

@M02885:307:000000000-CTYL9:1:1101:14863:1458 1:N:0:TAAGGCTA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:22916:1474 1:N:0:TAAGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:19462:1492 1:N:0:TATGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:22624:1502 1:N:0:TATGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:18965:1510 1:N:0:TAAGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!!

I think the tool cannot be applied for the sequencing design I mentioned above, as the primer sequences have a varied location within the reads (see the screenshot): primers_read1

XLZH commented 1 month ago

You are right, pTrimmer may not be a proper tool for your condition, because the forward primer sequence usually exists in the begging of the read in target/amplicon sequencing data!在 2024年7月15日，14:51，vera-rykalina @.***> 写道： I believe, it had been an outdated version that caused the issue. I could get all the output files, using version 1.4.0. However, all reads in the output files contain only N's. @M02885:307:000000000-CTYL9:1:1101:14863:1458 1:N:0:TAAGGCTA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:22916:1474 1:N:0:TAAGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:19462:1492 1:N:0:TATGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:22624:1502 1:N:0:TATGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! @M02885:307:000000000-CTYL9:1:1101:18965:1510 1:N:0:TAAGGCGA+CTATTAAT NNNNNNNNNNNNNNNNNNNN + !!!!!!!!!!!!!!!!!!!! I think the tool cannot be applied for the sequencing design I mentioned above, as the primer sequences have a varied location within the reads (see the screenshot): primers_read1.PNG (view on web)

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