mapleforest
commented
7 years ago Dear Sir,
It is strange. It appears there is no definition of the output unincorporated sequence,
but I can not pinpoint the problem with current information.
Can you send me all the log files pertinent to hm.batchB?
Have you successfully passed both example1 and 2?
You can use faDnaPolishing.pl to check if there are strange squences/characters in the genomic sequences.
Do you have more than 2000 scaffolds in your assembly? If so, more file handles should be assigned (see the manual).
在 2017/5/17 16:52, chklopp 写道:
While testing on a genome of interest hm.batchB3.haplomerger does not produce a correct output and in the _B3.haploMerger.log I get the following error
HM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. ...
The beginning of the file seem OK
Ch+
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best regards,
黄盛丰 Shengfeng Huang 中山大学生命科学学院 School of life sciences, Sun Yat-sen university hshengf2@mail.sysu.edu.cn http://sklbc.sysu.edu.cn/Team/User/info.aspx?typeid=283&pid=46
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chklopp
While testing on a genome of interest hm.batchB3.haplomerger does not produce a correct output and in the _B3.haploMerger.log I get the following error
HM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. Use of uninitialized value in length at ../bin/XHM_haploMerger.pl line 833. ...
The beginning of the file seem OK
Ch+