Error Reading Environment Data 14
Sign in Pricing Blog Support Search GitHub This repository Watch 367 Star 1,478 Fork 380 dotnet/cli Code Issues 757 Pull requests 18 Projects 1 Pulse Graphs New issue Error on "dotnet restore restore.dg" for ASP.Net Core Project in VS 2015 Update 3 with latest Dotnet CLI. #4248 Open DreamingDevs opened this Issue Sep 26, 2016 · 10 comments Projects None yet Labels None yet Milestone No milestone Assignees No one assigned 8 participants DreamingDevs commented Sep 26, 2016 • edited Hi, Steps to Reproduce Create a new ASP.Net Core application in Visual Studio Community 2015 Update 3 on Windows 10 with latest Dotnet CLI (preview3-003686) and VS Tooling (VS2015Tools.Preview2.0.2). Point nuget.config to aspnetcore-dev myget feed. Actual behavior When ever I create a new ASP.Net Core Project in Visual Studio community 2015 update 3, the first package restore (which happens immediately after project creation) fails with following error. In fact the same error is coming even if we do restore packages (by right clicking references of the project). PATH=.\node_modules\.bin;C:\Program Files (x86)\Microsoft Visual Studio 14.0\Web\External;%PATH%;C:\Program Files (x86)\Microsoft Visual Studio 14.0\Web\External\git C:\Program Files\dotnet\dotnet.exe restore "C:\Users\ramiadmin\Desktop\SampleApp\.vs\restore.dg" error: Error reading 'C:\Users\ramiadmin\Desktop\SampleApp\.vs\restore.dg' at line 0 column 0 : Unexpected character encountered while parsing value: #. Path '', line 0, position 0. error: Unexpected character encountered while parsing value: #. Path '', line 0, position 0. Interesting point it, if I dot dotnet restore from command line, it successfully restore all the packages. Also dotnet run from command line works absolutely fine. I pointed my nuget.config to aspnetcore-dev myget feed -
faq • rss Community Log In Sign Up Add New Post Question: Getting: Error reading _plen[] array: 1776466139, 4294967292 with TopHat2/bowtie2 0 https://www.biostars.org/p/135537/ 19 months ago by rubic • 60 United States rubic • 60 wrote: Hi, I think seem to be doing something very basically wrong in running TopHat2 so it's probably an easy answer. Here's my command: tophat --read-mismatches 1 --output-dir /n/user/rubi/data/tophat.alns/s1/s1 --num-threads 8 --transcriptome-index /n/user/rubi/refdata/tophat.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 /n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 /n/user/rubi/data/fq/s1.fq Here's the log file: [2015-03-20 00:07:34] Beginning error reading TopHat run (v2.0.4) ----------------------------------------------- [2015-03-20 00:07:34] Checking for Bowtie Bowtie version: 2.0.0.6 [2015-03-20 00:07:34] Checking for Samtools Samtools version: 0.1.12.a [2015-03-20 00:07:34] Checking for Bowtie index files [2015-03-20 00:07:34] Checking for Bowtie index files [2015-03-20 00:07:34] Checking for reference FASTA file [2015-03-20 00:07:34] Generating SAM header for /n/user/rubi/refdata/tophat.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 format: fastq quality scale: phred33 (default) [2015-03-20 00:07:35] Reading known junctions error reading environment from GTF file [2015-03-20 00:08:03] Preparing reads left reads: min. length=20, max. length=59, 128844351 kept reads (192369 discarded) [2015-03-20 00:49:52] Using pre-built transcriptome index.. [2015-03-20 00:50:20] Mapping left_kept_reads to transcriptome mm10 with Bowtie2 [2015-03-20 03:33:13] Resuming TopHat pipeline with unmapped reads [2015-03-20 03:33:15] Mapping left_kept_reads.m2g_um to genome mm10 with Bowtie2 [FAILED] Error running bowtie: Error reading _plen[] array: 1776466139, 4294967292 Error: Encountered internal Bowtie 2 exception (#1) Command: /n/sw/bowtie2-2.0.0-beta6/bowtie2-align -q -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min L,-0.6,-0.6 -p 8 --sam-no-hd -x /n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10/mm10 - As far as I can tell BOWTIE_INDEXES is defined as an environment variable: rubi@rclogin09 10:25 ~ >echo $BOWTIE_INDEXES /n/user/rubi/refdata/bowtie.2.gencode.vM2.annotation.2wayconspseudos.mm10 And the transcriptome and genome indix folders seem to be found - according to the log. So what's wrong? bowtie rna-seq tophat • 1.1k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 17 months ago by Biostar ♦♦ 0 • written 19 month