我有一些BAM格式的芯片seq数据 在某些时候，我想做一个de novo motif discovery 使用HOMERs findMotifsGenome.pl脚本
问题似乎是这个应用程序无法打开refrence基因组fasta文件，即使它们是由应用程序本身安装的！
有没有人遇到过这个问题？
$ perl /home/chipseq_project/homer/bin/findMotifsGenome.pl /home/chipseq_project/homer/findpeak_output/peaks.txt hg19 / home / chipseq_project / homer / motif_output / -size given
Position file = /home/chipseq_project/homer/findpeak_output/peaks.txt
Genome = hg19
Output Directory = /home/chipseq_project/homer/motif_output/
Using actual sizes of regions (-size given)
Fragment size set to given
Found mset for "human", will check against vertebrates motifs
Peak/BED file conversion summary:
BED/Header formatted lines: 0
peakfile formatted lines: 7662
Peak File Statistics:
Total Peaks: 7662
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background fragment size set to 81 (avg size of targets)
Background files for 81 bp fragments found.
Extracting sequences from directory: /home/chipseq_project/homer/.//data/genomes/hg19//
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Not removing redundant sequences
Sequences processed:
0 total
Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8
Freq Bin Count
Total sequences set to 50000
Choosing background that matches in CpG/GC Content...
在/home/chipseq_project/homer/bin/assignGeneWeights.pl第63行非法除零。 装配序列文件...... 使用homer2归一化低阶寡核苷酸
Reading input files...
0 total sequences read
Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Normalization weights can be found in file: /home/chipseq_project/homer/motif_output//seq.autonorm.tsv
Converging on autonormalization solution:
...............................................................................
Final normalization: Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Finished preparing sequence/group files
----------------------------------------------------------
Known motif enrichment
Reading input files...
0 total sequences read
264 motifs loaded
Cache length = 11180
Using binomial scoring
Checking enrichment of 264 motif(s)
|0% 50% 100%|
/home/chipseq_project/homer/bin/findKnownMotifs.pl第142行非法除零。 -------------------------------------------------- -------- 重新发现主题（HOMER）
Scanning input files...
!!!出了点问题......你确定你选择了合适的长度来寻找主题吗？ ！即检查您的序列文件!!!
Scanning input files...
!!!出了点问题......你确定你选择了合适的长度来寻找主题吗？ ！即检查您的序列文件!!!
-blen automatically set to 2
Scanning input files...
!!!出了点问题......你确定你选择了合适的长度来寻找主题吗？ ！即检查你的序列文件！ 在/home/chipseq_project/homer/bin/compareMotifs.pl第1289行的数字gt（＆gt;）中使用未初始化的值。 ！过滤掉所有图案!!! 工作完成 - 如果结果看起来不错，请将啤酒送到..
Cleaning up tmp files...
答案 0 :(得分：1)
要检查的一件事：如果您的床文件中的染色体命名与您正在使用的基因组中的染色体命名一致：例如，您的床文件中的12号染色体不应该为'12'，而在您的基因组中感兴趣的是'chr12'
答案 1 :(得分：0)
＆＃34; chr＆＃34;问题，简单的awk命令你的朋友。简单的awk＆＃39; {print＆＃34; chr＆＃34; $ 0}＆＃39; your.bed＆gt; your_new.bed将完成这项工作。 hkoohy
答案 2 :(得分：0)
我也遇到了这个问题，而且我的 BED 文件也很好。但是，解决它的技巧是通过以下代码将我的 .bed 文件更改为 .pos 文件：
bed2pos.pl file.bed > file.pos
我希望这对你们有帮助:)
最好的芙蓉