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mapleforest / HaploMerger2

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Got an error when I ran the example3 #23

Open Haoran-Xue opened 5 years ago

Haoran-Xue commented 5 years ago

Hello,

When I ran the example3. Everything went well, until I ran batchD3 like this:

./hm.batchD3.remove_tandem_assemblies bbv18wm_A_ref_C

Here are what displayed on the screen:

Running command : ./hm.batchD3.remove_tandem_assemblies bbv18wm_A_ref_C

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

These files/directories are going to be output : bbv18wm_A_ref_C.bbv18wm_A_ref_Cx.result/selfOnly.nets/*.net - store the self-self notrivial net files (deletable) bbv18wm_A_ref_C.bbv18wm_A_ref_Cx.result/hm.tandem_assemblies - show tandem positions *** bbv18wm_A_ref_C_D.fa.gz - the new haploid genome assembly withf tandem mis-assemblies removed log files: _D3.tandem_removal.log (including the info of removed seqeunces) _D3.tandem_removal_excised_seq.fa (including the excised sequences)

mv: cannot stat ‘bbv18wm_A_ref_C_rt.fa.gz’: No such file or directory

I cannot find bbv18wm_A_ref_C_rt.fa.gz either. Do you know how (in which step) it should be generated?

mapleforest commented 5 years ago

sorry I need all the output to pinpoint the problem. It is supposed to go smooth with example3. You may make sure run it step by step and make sure if the previous steps are correctly executed.

Haoran-Xue commented 5 years ago

I found the problem. It happened at C1. getopts.pl is missing.

Here is what _C1.scaffolding.log looks like:

Can't locate getopts.pl in @INC (@INC contains: /ohta/haoran.xue/programs/HaploMerger2_20180603/SSPACE-STANDARD-3.0_linux-x86_64/dotlib/ /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ../SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl line 124.