运行报错 merge_repeatMasker_out.pl line 40 #20
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估计你这边运行时，没有加repeatmasker的species参数，并用了最新版本。有这个bug的。推荐用git clone命令下载最新版本，比压缩包更新，解决了该bug的。
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主题: [chenlianfu/geta] 运行报错 merge_repeatMasker_out.pl line 40 (Issue #20)
您好，我想求助一下，我在开始运行之后，出现了以下报错，这是什么原因呢，请问这样怎么解决呀？
No such file or directory at ~/geta-master/bin/merge_repeatMasker_out.pl line 40.
failed to execute: ~/geta-master/bin/merge_repeatMasker_out.pl ~/cevi.tmp/genome.fasta repeatMasker/RepeatMasker_out.out repeatModeler/RepeatModeler_out.out > genome.repeat.stats
CMD: /geta-master/bin/ParaFly -c/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/ParaFly.log
CMD: ~/geta-master/bin/ParaFly -c ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/ParaFly.log
Can not open file ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at /geta-master/bin/para_RepeatMasker line 138.
Can not open file/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at ~/geta-master/bin/para_RepeatMasker line 138.
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并且再次运行时，将repeatmasker中间文件夹删除，再继续运行。
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主题: [chenlianfu/geta] 运行报错 merge_repeatMasker_out.pl line 40 (Issue #20)
您好，我想求助一下，我在开始运行之后，出现了以下报错，这是什么原因呢，请问这样怎么解决呀？
No such file or directory at ~/geta-master/bin/merge_repeatMasker_out.pl line 40.
failed to execute: ~/geta-master/bin/merge_repeatMasker_out.pl ~/cevi.tmp/genome.fasta repeatMasker/RepeatMasker_out.out repeatModeler/RepeatModeler_out.out > genome.repeat.stats
CMD: /geta-master/bin/ParaFly -c/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/ParaFly.log
CMD: ~/geta-master/bin/ParaFly -c ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/ParaFly.log
Can not open file ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at /geta-master/bin/para_RepeatMasker line 138.
Can not open file/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at ~/geta-master/bin/para_RepeatMasker line 138.
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老师，您好，我能否不调用Repeatmasker，直接输入一个masked之后的基因组运行呢 |
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直接运行程序是不行的。间接是可以的。你可以将该基因组fasta文件顶替相应中间文件即可。
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主题: Re: [chenlianfu/geta] 运行报错 merge_repeatMasker_out.pl line 40 (Issue #20)
老师，您好，我能否不调用Repeatmasker，直接输入一个masked之后的基因组运行呢
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出了顶替文件，还要生成相应.ok文件，不让repeatmasker和repeatmodeler步骤运行。其实不推荐这样做。geta只屏蔽转座子序列，并没有屏蔽串联重复。若是输入的基因组序列屏蔽了串联重复，是不推荐的做法。
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主题: Re: [chenlianfu/geta] 运行报错 merge_repeatMasker_out.pl line 40 (Issue #20)
老师，您好，我能否不调用Repeatmasker，直接输入一个masked之后的基因组运行呢
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哦哦，这样啊，老师；我重新改了下命令，如下： |
嗯嗯，明白啦，那还是按照老师的建议，全程使用geta来进行。 |
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你手工将那个文件夹和文件生成即可
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主题: Re: [chenlianfu/geta] 运行报错 merge_repeatMasker_out.pl line 40 (Issue #20)
哦哦，这样啊，老师；我重新改了下命令，如下：
nohup geta.pl --genome Viridiplantae --genome genome.fasta -1 libb.1.fq.gz -2 libb.2.fq.gz --protein homolog.fasta --augustus_species chlamydomonas --out_prefix cevi --cpu 72 --RM_lib consensi.fa.classified --gene_prefix CeviGene --pfam_db Pfam-AB.hmm &
报错 这样：
touch: 无法创建'repeatMasker/genome.fasta.out': 没有那个文件或目录
failed to execute: touch repeatMasker/genome.fasta.out
请问老师，这样如何解决呢
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老师，我试了下老版本也是报类似的错误，我的git clone似乎不太好用，您能给我一个2.5.6修复bug的版本的下载链接么，谢谢老师啦 |
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您好，我想求助一下，我在开始运行之后，出现了以下报错，这是什么原因呢，请问这样怎么解决呀？
No such file or directory at ~/geta-master/bin/merge_repeatMasker_out.pl line 40.
failed to execute: ~/geta-master/bin/merge_repeatMasker_out.pl ~/cevi.tmp/genome.fasta repeatMasker/RepeatMasker_out.out repeatModeler/RepeatModeler_out.out > genome.repeat.stats
CMD:
/geta-master/bin/ParaFly -c/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/ParaFly.logCMD: ~/geta-master/bin/ParaFly -c ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/command.RepeatMasker.list -CPU 27 &> ~/cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/ParaFly.log
Can not open file ~/cevi.tmp/0.RepeatMasker/repeatMasker/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at
/geta-master/bin/para_RepeatMasker line 138./cevi.tmp/0.RepeatMasker/repeatModeler/para_RepeatMasker.tmp/seq_1/seq_1.fasta.out, No such file or directory at ~/geta-master/bin/para_RepeatMasker line 138.Can not open file
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