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Tophat Error While Flushing And Closing Output

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length=50, 2260990 kept reads (2 discarded) [2015-02-24 22:02:35] Mapping left_kept_reads to genome Athaliana with Bowtie2          [FAILED] Error running bowtie: Error while flushing and closing output Error while Send to Email Address Your Name Your Email Address Cancel Post was not sent - check your email addresses! error in tophat2 hi, I have already built index for genome fasta by **bowtie2-build genome.fa aspergillus.fumigat... bowtie could not build the index sorry guys, i was building transcriptom index: i have yeast_SGD_anno.gtf and orf_coding.fasta as... this contact form

tophat2 --... I'm getting this error from tophat: samtools: writing to standard output failed: ... Warning: junction database is empty! Error: segment-based junction search failed with err =127   tophat2 mapping error I always use this command and mapping is successfully end. http://seqanswers.com/forums/showthread.php?t=15599

Error While Flushing And Closing Output

Please refer to our Privacy Policy or Contact Us for more details You seem to have CSS turned off. Jonathan Moore Others have found this problem (me included). [email protected]:~/src/tools/test_data$ tophat2... about • faq • rss Community Log In Sign Up Add New Post Question: ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2 0 19 months ago by catherine12243 •

Most of errors seem to relate to the reference: Is your reference specifically indexed for Bowtie2?  An unindexed reference or a reference indexed for Bowtie1 won't work. length=101, 11239076 kept reads (363723 discarded) [2014-06-10 11:01:18] Mapping left_kept_reads to genome hg19 with Bowtie2 [2014-06-10 11:27:15] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4) [2014-06-10 11:28:40] Mapping left_kept_reads_seg2 to genome Hi all,  I ran tophat on my fastq file and I got the following error: [2015-09-02 11:23:58] Beg... Any other ideas on how to solve it?

Please don't fill out this field. Tophat Building transcriptome files synthax Hello, I need to create the Tophat reference index of the human genome. Tophat developers are working to address this issue. my company Although I'm very inexperienced with bioinformatics, what I"m trying to do is very straightforwar...

All help is greatly appreciated! Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Any clues? Seems like an easy fix, but no..

Error While Flushing And Closing Output Bowtie

length=101, 11239076 kept reads (363723 discarded) [2014-06-10 11:01:18] Mapping left_kept_reads to genome hg19 with Bowtie2 [2014-06-10 11:27:15] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4) [2014-06-10 11:28:40] Mapping left_kept_reads_seg2 to genome https://www.biostars.org/p/132408/ All Rights Reserved. Error While Flushing And Closing Output thanks, Adi [2014-06-10 10:01:48] Beginning TopHat run (v2.0.11) [2014-06-10 10:01:48] Checking for Bowtie Bowtie version: 2.2.3.0 [2014-06-10 10:01:48] Checking for Samtools Samtools version: 0.1.19.0 [2014-06-10 10:01:48] Checking for Bowtie index files Bowtie2-align Died With Signal 6 (abrt) (core Dumped) Terms Privacy Opt Out Choices Advertise Get latest updates about Open Source Projects, Conferences and News.

Suffice it to say that I have, thus far, not been impressed with Bowtie2/Tophat. weblink Similar Threads Thread Thread Starter Forum Replies Last Post TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/. Error running bowtie: .. (When I use tophat2) Hi I was install bowtie2(apt-get install bowtie, bowtie2, samtools) and version is /usr/bin/b... Did you ever solve this problem? Bowtie2-align Died With Signal 13 (pipe)

Error: segment-based junction search failed with err =-5 Hello, I am new to using tophat and bowtie for RNA-seq data. Sign up for the SourceForge newsletter: I agree to receive quotes, newsletters and other information from sourceforge.net and its partners regarding IT services and products. Aborted (core dumped) Forum: Bowtie Help Creator: Jeremy D Zucker Created: 2014-11-05 Updated: 2014-11-05 Jeremy D Zucker - 2014-11-05 Hi folks, I am running Bowtie from within Trinity, and I ran navigate here However it is not yet compatible with tophat.

Low final mapping rate by TopHat in spite of high initial Bowtie mapping Hi,  I am running TopHat2/2.0.14 using this code: tophat \ --transcriptome-index "${tra... If this happens consistently with a certain set of inputs, could you make the inputs available to me so that I can try to reproduce? Matt MacManes cool!

Found both Bowtie1 and Bowtie2 indexes. [2014-06-06 13:29:08] Checking for reference FASTA file [2014-06-06 13:29:08] Generating SAM header for allchr [2014-06-06 13:29:08] Preparing reads left reads: min.

length=101, 250 kept reads (0 discarded) right reads: min. Error running /usr/local/bin/tophat_reports Greetings: I am currently getting an error: [2016-06-20 11:21:43] Beginning TopHat run... Thank you guys so much for the help! Tophat error : Error: gtf_to_fasta returned an error.

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I understand that I can withdraw my consent at any time. It couldn't work and report... Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. tophat2 stopped at bowtie step Here is the problem I have two paired read files, each with only 250 reads (so memory is not an ...

I tried both the linux executable and I compiled bowtie2 from source for version 2.2.3.0 and the error is still there. Tophat2 output error I am trying to run a basic Tophat2 command but it goes wrong somewhere. ADD REPLY • link written 2.4 years ago by Devon Ryan ♦ 57k just tried, does not work. I'm using the pre-built executables of Tophat, and I'm trying to run the test in the Tophat manual ("Testing the installation"), which is where I get the error.

ErikFas View Public Profile Send a private message to ErikFas Find More Posts by ErikFas 06-18-2014, 02:43 AM #5 edm1 Member Location: UK Join Date: May 2013 Posts: 10 The version in use is v2.1.1 (tophat2). The bug was reported, claimed fixed, but it not.. Last edit: Jeremy D Zucker 2014-11-05 If you would like to refer to this comment somewhere else in this project, copy and paste the following link: SourceForge About Site Status @sfnet_ops

To see what the indexing step of the transcriptome failed, look in the run log to find the exact command run and then run that yourself (hopefully the ./tophat_out/tmp/h_sapiens_37_asm.fa files still I ended up using STAR, which I think may be better anyway. Please refer to our Privacy Policy or Contact Us for more details You seem to have CSS turned off. length=151, max.

Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc. I would have thought that these very popular software packages would have been tighter.. but encountered some errors. [email protected]:/mnt/data3/macmanes/tophat$ tophat -p8 -o 2926 pero ../pero_annotation/Pero2926.1.fastq ../pero_annotation/Pero2926.2.fastq [2014-05-28 07:46:31] Beginning TopHat run (v2.0.11) ----------------------------------------------- [2014-05-28 07:46:31] Checking for Bowtie Bowtie version: 2.2.2.0 [2014-05-28 07:46:31] Checking for Samtools Samtools version: 0.1.19.0

Tophat runs through without errors but no read mapped Hello, I am a new user of tophat. I used default parame... Enraico View Public Profile Send a private message to Enraico Find More Posts by Enraico 06-09-2014, 09:51 AM #3 tulipnandu Junior Member Location: Dallas Join Date: Feb 2013 Posts: