Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas Re: [Inchworm-users] Max Kmer size From: Brian J Haas
GenoMax11-03-2014, 07:19 AMThe command should be (I was going off what you had in your prior post) $ samtools mpileup -uf $BT2_HOME/example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -O u - > eg2.raw.bcf Commands such as halt, poweroff, reboot will return command not found. Best regards Zillur GenoMax11-03-2014, 03:58 AMYou need to add execute permissions to the new bcftools executable. $ chmod u+x /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1/bcftools/bcftools zillur11-03-2014, 05:19 AMThank you very much. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > Inchworm-users mailing list http://superuser.com/questions/435988/how-can-i-resolve-the-error-cannot-execute-binary-file
Please don't fill out this field. naccess download error Gizem-iMac:Naccess gizemtatar$ csh install.scr $ naccess installation program $ ----------------... Should I be doing anything > differently to maximize Inchworm's potential to assemble transcripts? If you try to go beyond 32, your still only storing a 32mer worth of sequence and tossing out the other bits.
share|improve this answer answered Jun 12 '12 at 22:29 acoh Facha 1674 add a comment| Your Answer draft saved draft discarded Sign up or log in Sign up using Google DownloadingÂ https://do... Best Regards Zillur zillur11-04-2014, 05:04 AM[QUOTE=GenoMax;153671]This is a simple work around. Cannot Execute Binary File Ubuntu the error is here: >> >>> /usr/sbin/grub-install: /usr/sbin/grub-install: cannot execute binary >>> file >>> /usr/sbin/grub-probe: error: cannot find a device for / (is /dev >>> mounted?). >> >> >> David >
Dear all, I 'm trying to run the script: align_and_estimate_abundance.pl with the comand: /usr/... Cannot Execute Binary File Exec Format Error Ubuntu I need instructions on what's next after unzip. Normally, it should look like !/bin/bash or /usr/bin/perl, or whatever is intended to use for executing it. Premier dating websites with free messaging usa dating a friend during divorce york nous engageons sur js for Raspberry Pi GitHub server - debugging with dating usa regeln sommerzeit rencontre en
I aligned the example lambda virus. Cannot Execute Binary File Exec Format Error Cygwin I am asking you mentioning my details files and folders cause I don't another mess. I'm using a Mac. Try booting the system in single-user mode (might be labelled as recovery mode) and see if you can get to a root shell. –Darth Android Jun 12 '12 at 21:51 2
Does the blat pipeline only add these for stranded reads ? Here is my command line on terminal: Mds-MacBook-Pro:bioinformatics ZILLURRAHMAN$ cd bow-tie Mds-MacBook-Pro:bow-tie ZILLURRAHMAN$ ls 2012_Lab_Exercise_2.doc CGRL - Installing and Using Bowtie.webarchive How to install Bowtie - SEQanswers.webarchive Installation and use of Cannot Execute Binary File In Linux Error FrameDP installation issue Has anyone ever encountered issues installing FrameDP on a local computer? Cannot Execute Binary File Mac A new version of Inchworm is now available here: http://sourceforge.net/projects/inchworm/files/inchworm_r02-21-2011.tgz/download It includes the following changes: -cannot seed contigs from palindromic kmers -in double-stranded mode, the reverse-complement kmers are disabled during path
Mds-MacBook-Pro:~ ZILLURRAHMAN$ vi -bash: vi: command not found Mds-MacBook-Pro:~ ZILLURRAHMAN$ vim -bash: vim: command not found Mds-MacBook-Pro:~ ZILLURRAHMAN$ -vi -bash: -vi: command not found Mds-MacBook-Pro:~ ZILLURRAHMAN$ blancha10-18-2014, 08:46 AMJust type the http://ibuildsystem.com/cannot-execute/usr-bin-vim-cannot-execute-binary-file.php It did not work for me as no make file in the unzip folder. Stop. 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 Cannot Execute Binary File Java
At this point you could check a couple more locations from this thread (last post in the thread): https://discussions.apple.com/thread/2651443?start=0&tstart=0 Those are /etc/profile and /etc/bashrc. Tango Icons © Tango Desktop Project. I have type the followings but....... navigate here Hopefully, you have enough physical RAM, which we estimate at around 1G of RAM per 1 M reads (~100 base), which in your case might require ~50G of RAM.
zillur11-02-2014, 07:14 AMThank you very much. Java Cannot Execute Binary File: Exec Format Error dp05yk05-25-2011, 08:54 PMStrange... I'm > wondering if it's still doing anything?
BTW, you would do well to buy a book on using Linux (or Unix or even Mac OS X from the command line). VCFtools installtion error I am trying to install Vcftools and getting this error even after installing the required C compi... I tried to re-download the file and now the unzip commend works! Bash Cannot Execute Binary File Ubuntu zillur11-04-2014, 05:16 AMThank you very much.
We'll continue to maintain both sites, since there are additional Inchworm-based applications that haven't been migrated over to Trinity just yet, such as genome-guided de novo transcript assembly and integration with simobioinfo08-04-2014, 08:03 AMThank you and excuse me but I registered to the site just few minutes ago. Using an editor I created a text file where I set the path for bowtie2, smalls, bcftools. his comment is here See it anyway?
Haas Manager, Genome Annotation Research and Development The Broad Institute http://broad.mit.edu/~bhaas [Inchworm-users] XS tags in non-strand-specific blat alignments From: Thomas Sandmann
Best, -brian > Also, I'm hoping to submit this data for publication in the near future, is > there an ETA on a date for a publication that I can cite? What does it mean? If so, I'll plan for a new release shortly. executable - bash a precompiled version of dawn binary which will run on microsoft windows.
I just don't want to create path every time I am opening a new shell. Also, I encourage you to use trinity as opposed to just inchworm. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Haas > Manager, Genome Annotation Research and Development > The Broad Institute > http://broad.mit.edu/~bhaas > > > > > -- -- Brian J.
In many > cases, we end up getting an ever so slight increase in the number of > full-length transcripts. > > >> 2. Adv Reply May 30th, 2012 #5 ertansinansahin View Profile View Forum Posts Private Message First Cup of Ubuntu Join Date May 2012 Beans 11 Re: Error: "cannot execute binary file"