Can't install MitoFinder

[Flowmatics]

Hi,

I am quite thrilled about MitoFinder and wanted to install this week. Unfortunately I got an error. It is strange. Apparently the script is looking for something which is not there. I tried to fix it with a colleague but we were not able to get it running. Can you help us? Please find the log below:

florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ./install.sh ./build.sh: line 1: aclocal: command not found ./build.sh: line 2: autoconf: command not found ./build.sh: line 3: automake: command not found ./build.sh: line 4: ./configure: No such file or directory make: No rule to make target 'clean'. Stop. make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cat install.sh chmod 764 /// chmod 764 // chmod 764 / chmod 764 cd idba ./build.sh cd .. cd metaSpades/bin/ p=$(pwd) ln -s "$p"/spades.py "$p"/metaspades.py cd ../../ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cd idba/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 build.sh configure.ac install-sh NEWS stamp-h1 AUTHORS ChangeLog depcomp lib README.md test bin config.h Dockerfile Makefile.am script WORKSPACE BUILD config.h.in gtest_src missing src florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./build.sh ./build.sh: line 1: aclocal: command not found ./build.sh: line 2: autoconf: command not found ./build.sh: line 3: automake: command not found ./build.sh: line 4: ./configure: No such file or directory make: No rule to make target 'clean'. Stop. make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ cd.. cd..: command not found florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 build.sh configure.ac install-sh NEWS stamp-h1 AUTHORS ChangeLog depcomp lib README.md test bin config.h Dockerfile Makefile.am script WORKSPACE BUILD config.h.in gtest_src missing src florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio megahit blast metaSpades CHANGELOG mitofinder circularizationCheck.py Mitofinder.config circularizationCheck.pyc README.md export_mitochondrial_contigs.py rename_fasta_seqID.py extract_genes.py runIDBA.py extract_seq.py runIDBA.pyc FirstBuildChecker.py runMegahit.py FirstBuildChecker.pyc runMegahit.pyc genbankOutput.py runMetaspades.py genbankOutput.pyc runMetaspades.pyc geneChecker_fasta.py sort_gff.py geneChecker.py testcase geneChecker.pyc tRNAscan idba tRNAscanChecker_arwen.py image tRNAscanChecker.py install.sh tRNAscanChecker.pyc florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ make clean make: No rule to make target 'clean'. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ make make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cd Bio/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/Bio$ ls Affy FSSP NeuralNetwork SeqRecord.py Align GA Nexus SeqRecord.pyc AlignIO GenBank NMR Sequencing Alphabet Geo pairwise2.py SeqUtils Application Graphics ParserSupport.py Statistics bgzf.py HMM ParserSupport.pyc SubsMat bgzf.pyc HotRand.py Pathway SVDSuperimposer Blast Index.py PDB SwissProt CAPS init.py Phylo TogoWS Cluster init.pyc PopGen trie.c Compass KDTree _py3k triefind.py cpairwise2module.c KEGG Restriction trie.h Crystal kNN.py SCOP triemodule.c Data LogisticRegression.py SearchIO UniGene DocSQL.py MarkovModel.py Search.py UniProt Emboss MaxEntropy.py SeqFeature.py _utils.py Entrez Medline SeqFeature.pyc _utils.pyc ExPASy Motif SeqIO Wise File.py motifs Seq.py File.pyc NaiveBayes.py Seq.pyc florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/Bio$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio megahit blast metaSpades CHANGELOG mitofinder circularizationCheck.py Mitofinder.config circularizationCheck.pyc README.md export_mitochondrial_contigs.py rename_fasta_seqID.py extract_genes.py runIDBA.py extract_seq.py runIDBA.pyc FirstBuildChecker.py runMegahit.py FirstBuildChecker.pyc runMegahit.pyc genbankOutput.py runMetaspades.py genbankOutput.pyc runMetaspades.pyc geneChecker_fasta.py sort_gff.py geneChecker.py testcase geneChecker.pyc tRNAscan idba tRNAscanChecker_arwen.py image tRNAscanChecker.py install.sh tRNAscanChecker.pyc florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ./install.sh ./build.sh: line 1: aclocal: command not found ./build.sh: line 2: autoconf: command not found ./build.sh: line 3: automake: command not found ./build.sh: line 4: ./configure: No such file or directory make: No rule to make target 'clean'. Stop. make: No targets specified and no makefile found. Stop. ln: failed to create symbolic link '/home/florian/Downloads/MitoFinder-master/metaSpades/bin/metaspades.py': File exists florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ emacs install.sh -nwflorian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ which bash /bin/bash florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ emacs install.sh -nwflorian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ./install.sh bash: ./install.sh: /usr/bin/bash: bad interpreter: No such file or directory florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ emacs install.sh -nwflorian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ./install.sh ./build.sh: line 1: aclocal: command not found ./build.sh: line 2: autoconf: command not found ./build.sh: line 3: automake: command not found ./build.sh: line 4: ./configure: No such file or directory make: No rule to make target 'clean'. Stop. make: No targets specified and no makefile found. Stop. ln: failed to create symbolic link '/home/florian/Downloads/MitoFinder-master/metaSpades/bin/metaspades.py': File exists florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cat install.sh

!/bin/bash

chmod 764 /// chmod 764 // chmod 764 / chmod 764 cd idba ./build.sh cd .. cd metaSpades/bin/ p=$(pwd) ln -s "$p"/spades.py "$p"/metaspades.py cd ../../ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio megahit blast metaSpades CHANGELOG mitofinder circularizationCheck.py Mitofinder.config circularizationCheck.pyc README.md export_mitochondrial_contigs.py rename_fasta_seqID.py extract_genes.py runIDBA.py extract_seq.py runIDBA.pyc FirstBuildChecker.py runMegahit.py FirstBuildChecker.pyc runMegahit.pyc genbankOutput.py runMetaspades.py genbankOutput.pyc runMetaspades.pyc geneChecker_fasta.py sort_gff.py geneChecker.py testcase geneChecker.pyc tRNAscan idba tRNAscanChecker_arwen.py image tRNAscanChecker.py install.sh tRNAscanChecker.pyc install.sh~ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cd idba/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 build.sh configure.ac install-sh NEWS stamp-h1 AUTHORS ChangeLog depcomp lib README.md test bin config.h Dockerfile Makefile.am script WORKSPACE BUILD config.h.in gtest_src missing src florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./config.h ./config.h: line 1: /bin: Is a directory ./config.h: line 2: /bin: Is a directory ./config.h: command substitution: line 4: unexpected EOF while looking for matching '' ./config.h: command substitution: line 14: syntax error: unexpected end of file ./config.h: line 4: /bin: Is a directory ./config.h: line 73: unexpected EOF while looking for matching'' ./config.h: line 75: syntax error: unexpected end of file florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ lsls

Command 'lsls' not found, did you mean:

command 'fsls' from deb python-fs command 'lsns' from deb util-linux

Try: sudo apt install

florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 bin build.sh config.h configure.ac Dockerfile install-sh Makefile.am NEWS script stamp-h1 WORKSPACE AUTHORS BUILD ChangeLog config.h.in depcomp gtest_src lib missing README.md src test florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./configure bash: ./configure: No such file or directory florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ less install-sh florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ less README.md florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./configure.ac ./configure.ac: line 4: syntax error near unexpected token 2.59' ./configure.ac: line 4:AC_PREREQ(2.59)' florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./configure bash: ./configure: No such file or directory florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ make make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 bin build.sh config.h configure.ac Dockerfile install-sh Makefile.am NEWS script stamp-h1 WORKSPACE AUTHORS BUILD ChangeLog config.h.in depcomp gtest_src lib missing README.md src test florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ less install-sh florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ./install-sh ./install-sh: no input file specified. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ cd bin/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/bin$ ls Makefile.am florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/bin$ make make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/bin$ ls Makefile.am florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/bin$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 bin build.sh config.h configure.ac Dockerfile install-sh Makefile.am NEWS script stamp-h1 WORKSPACE AUTHORS BUILD ChangeLog config.h.in depcomp gtest_src lib missing README.md src test florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ cd src/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/src$ ls assembly basic container graph misc release sequence test tools florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba/src$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ l saclocal.m4 BUILD config.h depcomp install-sh missing script/ test/ AUTHORS build.sh config.h.in Dockerfile lib/ NEWS src/ WORKSPACE bin/ ChangeLog configure.ac gtest_src/ Makefile.am README.md stamp-h1* florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ less BUILD florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ ls aclocal.m4 bin build.sh config.h configure.ac Dockerfile install-sh Makefile.am NEWS script stamp-h1 WORKSPACE AUTHORS BUILD ChangeLog config.h.in depcomp gtest_src lib missing README.md src test florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/idba$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ make make: No targets specified and no makefile found. Stop. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ös ös: command not found florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cd .. florian@florian-ThinkPad-P50:~/Downloads$ ls Fake-Gelelektrophorese.pdf MitoFinder-master MitoFinder-master.zip florian@florian-ThinkPad-P50:~/Downloads$ cd MitoFinder-master/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ less CHANGELOG florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ sh install.sh ./build.sh: 1: ./build.sh: aclocal: not found ./build.sh: 2: ./build.sh: autoconf: not found ./build.sh: 3: ./build.sh: automake: not found ./build.sh: 4: ./build.sh: ./configure: not found make: No rule to make target 'clean'. Stop. make: No targets specified and no makefile found. Stop. ln: failed to create symbolic link '/home/florian/Downloads/MitoFinder-master/metaSpades/bin/metaspades.py': File exists florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ cd blast/ florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/blast$ ls bin ChangeLog doc LICENSE ncbi_package_info README florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master/blast$ cd .. florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ less Mitofinder.config florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ less mitofinder florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ ls Bio FirstBuildChecker.py image rename_fasta_seqID.py testcase blast FirstBuildChecker.pyc install.sh runIDBA.py tRNAscan CHANGELOG genbankOutput.py install.sh~ runIDBA.pyc tRNAscanChecker_arwen.py circularizationCheck.py genbankOutput.pyc megahit runMegahit.py tRNAscanChecker.py circularizationCheck.pyc geneChecker_fasta.py metaSpades runMegahit.pyc tRNAscanChecker.pyc export_mitochondrial_contigs.py geneChecker.py mitofinder runMetaspades.py extract_genes.py geneChecker.pyc Mitofinder.config runMetaspades.pyc extract_seq.py idba README.md sort_gff.py florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$ sudo ./install.sh ./build.sh: line 1: aclocal: command not found ./build.sh: line 2: autoconf: command not found ./build.sh: line 3: automake: command not found ./build.sh: line 4: ./configure: No such file or directory make: No rule to make target 'clean'. Stop. make: *** No targets specified and no makefile found. Stop. ln: failed to create symbolic link '/home/florian/Downloads/MitoFinder-master/metaSpades/bin/metaspades.py': File exists florian@florian-ThinkPad-P50:~/Downloads/MitoFinder-master$

[RemiAllio]

Hello, Ok, it's a bit difficult for me to read your message (I don't understand why some lines are crossed out) but it seems that automake is not installed on your computer. To install it you can run the following command:

sudo apt-get install automake

So, please, could you install automake, rerun the installation, and tell me if it solved the installation problem.

Best regards, Rémi

N.B.: Given that the error is specific to IDBA-UD, you should be able to use MitoFinder with MetaSPAdes or MEGAHIT.

[Flowmatics]

Hi! Thank you for the quick response. Sorry for the strange crossed out lines, I don't know why it looks so strange. automake was really not installed, I tried it and problem is solved.

Thank you!