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The strand-specific data helps mostly in the cases where you have high gene density (some fungal genomes) and when transcripts slightly overlap from opposite strands. Adv Reply May 30th, 2012 #2 jonedney View Profile View Forum Posts Private Message Just Give Me the Beans! command line python script run on a file in different directory I have a script.py in /Users/admin/Desktop and I want to run this script on a file that is in /Us... Thanks! Source

Browse other questions tagged linux bash ssh debian or ask your own question. Thanks ! > > Fabrice > > Le 18/02/2011 15:21, Brian J Haas a √©crit : > > Hi Fabrice, >> >> Thanks for the info. Be a part of the beta today > http://p.sf.net/sfu/msIE9-sfdev2dev > _______________________________________________ > Inchworm-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/inchworm-users > -- -- Brian J. Would you please >> check ? >> >> Best regards, >> >> Fabrice Legeai >> AphidBase >> >> >> ------------------------------------------------------------------------------ >> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: >>

Cannot Execute Binary File In Linux Error

Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas Re: [Inchworm-users] compilation problem From: Brian J Haas - 2011-02-18 14:36:25 Attachments: Message as HTML Fantastic! It's a silent command. –Ben Richards Jun 12 '12 at 21:57 | show 4 more comments 5 Answers 5 active oldest votes up vote 45 down vote accepted Usually that error See if it works for you. $ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u -v -c 5 -g hom - > eg2.raw.bcf PS: If you type $ bcftools I'll check into > the other issues you describe, since they sound very familiar. > > > thanks! > > -brian > > > > > On Fri, Oct 14, 2011

  • Once I got the right file, unzip it and then follow the instructions mentioned above was fine.
  • unzip: cannot find zipfile directory in one of bowtie-0.12.7-macos-10.5-x86_64.zip or bowtie-0.12.7-macos-10.5-x86_64.zip.zip, and cannot find bowtie-0.12.7-macos-10.5-x86_64.zip.ZIP, period.
  • Exclude regions with "^" prefix Subset options: -a, --trim-alt-alleles trim alternate alleles not seen in the subset -I, --no-update do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
  • Best Regards Zillur GenoMax11-05-2014, 09:28 AMNow I have to measure the quality of the data that we generated as vcc format.
  • could you check the system info?
  • Looks like Bowtie comes precompiled so there's no makefile.
  • I don't know what is happening here.

G 0 . Start a coup online without the government intervening Are keywords in resolv.conf case sensitive? gene_x05-25-2011, 09:27 PMOK. Cannot Execute Binary File Ubuntu not a dynamic executable Adv Reply May 30th, 2012 #6 gnusci View Profile View Forum Posts Private Message Visit Homepage Quad Shot of Ubuntu Join Date Aug 2007 Location Canada

Its working now. I've been using the previous version of inchworm (inchworm_01-20-2011) for de novo assembly of transcriptomic data from a non-model organism with no reference genome available. Regards Zillur GenoMax10-19-2014, 04:34 PMI added a new account and in this account everything is going fine. https://www.biostars.org/p/3270/ A 0 .

Usage: bcftools view [options] [region1 [...]] Output options: -G, --drop-genotypes drop individual genotype information (after subsetting if -s option set) -h/H, --header-only/--no-header print the header only/suppress the header in VCF Cannot Execute Binary File Exec Format Error Cygwin They work better when you close windows." "You have enemies? Is this expected ? Last login: Sun Nov 2 17:00:11 on ttys000 -bash: $: command not found Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type bowtie2 -bash: type: bowtie2: not found Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type samtools.1 -bash: type: samtools.1: not found

Cannot Execute Binary File Exec Format Error Ubuntu

Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls commands lambda_virus.3.bt2 lambdaout.4.bt2 eg2.bam lambda_virus.4.bt2 lambdaout.rev.1.bt2 eg2.raw.bcf lambda_virus.fa lambdaout.rev.2.bt2 eg2.sam lambda_virus.rev.1.bt2 nohup.out eg2.sorted.bam lambda_virus.rev.2.bt2 out egl.sam lambdaout.1.bt2 out.sam lambda_virus.1.bt2 lambdaout.2.bt2 lambda_virus.2.bt2 lambdaout.3.bt2 Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /example/reference/lambda_virus.fa http://www.pclinuxos.com/forum/index.php?topic=128985.30 But I can't do it using vi editor. Cannot Execute Binary File In Linux Error GenoMax10-19-2014, 01:23 [email protected]: Reboot your Mac before doing anything (e.g. Cannot Execute Binary File Mac Terms Privacy Opt Out Choices Advertise Get latest updates about Open Source Projects, Conferences and News.

Print a binary keyboard translation table to stdout use of special device files [no]exec (Dis)allow use of executable files [no]suid is command nohup file name substituted! 83, View binary files a this contact form Thanks everyone for your inputs! –superuser Jun 13 '12 at 4:18 add a comment| up vote 9 down vote Try to run it using ./executablefilename instead of using sh executablefilename. Now my files are Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ ls AUTHORS bam_plbuf.c faidx.c ChangeLog.old bam_plbuf.h faidx.o INSTALL bam_plbuf.o htslib-1.1 LICENSE bam_plcmd.c kaln.c Makefile bam_plcmd.o kaln.h Makefile.mingw bam_reheader.c kaln.o NEWS bam_reheader.o kprobaln.c README bam_rmdup.c kprobaln.h Would you please to give me some suggestions by which I can measure the quality of the data. Cannot Execute Binary File Java

so the reason I couldn't unzip the zip file is that it's incomplete.. I'll have to investigate this further. Then from terminal type "cd desktop", and then "ls", to view all files on your desktop. http://bovbjerg.net/cannot-execute/usr-bin-ld-cannot-execute-binary-file.php Guess I shouldn't trust the results from the K > 31 runs... > In my various tests, I've found that 25mers work very well for > transcriptome data and going higher

Using "source" command allows you to read the profile without having to log out then in. Java Cannot Execute Binary File: Exec Format Error Note: I am still not sure how you managed to get your system into this state. How to make bowtie available via PATH settings ?

In my terminal basic commands are not found like: mds-macbook-pro:~ ZILLURRAHMAN$ ls -bash: ls: command not found mds-macbook-pro:~ ZILLURRAHMAN$ env -bash: env: command not found mds-macbook-pro:~ ZILLURRAHMAN$ edit -bash: edit: command

I suppose a better starting point would be, what is the output of echo $PATH ? (edit: the export command is a way to define an environment variable in bash.) –Darth To start a new thread: http://seqanswers.com/forums/showpost.php?p=153769&postcount=9 lonesome_forager11-11-2014, 02:29 AMHello, I'm also having trouble [email protected] Message: previous - nextMonth: November 2014 Re: [trinity-users] Exe GNU/Linux, Jessie, no-systemd From: Neo Futur You have to download and compile bcftools from here: http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2/download zillur11-02-2014, 07:22 PMThank you very much. Bash Cannot Execute Binary File Ubuntu Is there a particular reason for this limit? 2.

I did update the code to rectify the error, and I took the > Werror out of the compilation. > > Could you do me a big favor and see if GenoMax10-15-2014, 08:25 AMWhat is $BT2_HOME set to? GenoMax09-26-2014, 09:27 AMYou are trying to run the program from the current folder which is the wrong folder (did you read about the concept of relative paths at the Korf UNIX http://bovbjerg.net/cannot-execute/usr-bin-ssh-cannot-execute-binary-file.php GenoMax11-01-2013, 08:47 AMI'm also trying to install bowtie.

wrote: >>> >>> On my own followup, below is the installation log, indicating >>> something major >>> is seriously amiss with installing jessie-tde live isos on a >>> virtualbox vm. >>> Similar posts • Search » How Can I Use The Sff_Extract In Mira3 For Example Copy A File From Bin To User Directory After following the instructions you gave me and I have installed a program for astrophysics. Normally, it should look like !/bin/bash or /usr/bin/perl, or whatever is intended to use for executing it.

How can I fix this? vBulletin ©2000 - 2016, Jelsoft Enterprises Ltd. Our animal model (a squid) has no sequenced genome, so I'm curious about how well inchworm assembles contigs without mapping the illumina reads to a genome. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud.

Typically the cause is running an executable on the wrong architecture - if you try to run x86 executables on an ARM CPU, this message comes up. GenoMax11-02-2014, 03:27 PMFrom where I can get the "bcftools" files? My strategy so far has been to run inchworm on the raw data with a range of >> Kmer sizes, from 25-37, concatenate those outputs and reassemble using the >> '--reassembleIworm' As a monk, can I use Deflect Missiles to protect my ally?

Mds-MacBook-Pro:~ ZILLURRAHMAN$ type bowtie2 bowtie2 is hashed (/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2) Using same trick can I make path for samtools? But I just typed the line in the terminal and its working now. Code: sudo Jon Edney Follower of Christ, Husband, Dad, Aspiring Linux & Web Developer @TheJonEdney | jonedney.com | Ubuntu Wiki JonEdney on Freenode in #UbuntuForums Adv Reply May 30th, gene_x05-26-2011, 06:57 AMI tried to download an linux version and it indeed solved the problem!

Best, -b On Tue, May 24, 2011 at 4:14 PM, Kurt Showmaker wrote: > Hello, > I am trying to install inchworm, and do not think it is installing > so the reason I couldn't unzip the zip file is that it's incomplete..