Activity for ngopt
-
Nicolas Plaza posted a comment on ticket #24
I have the same error. [a5] ERROR: Unable to identify any properly paired reads [a5] ERROR: Please check that you have provided at least one library of paired-end reads with names conforming to the Illumina read pair convention. I work in the bin directoy and the path ( same erro)
-
Benni posted a comment on ticket #24
The errors seems to be gone, when I work in this wd: ~/Desktop/a5_miseq_linux_20160825 instead of /bin
-
I also get the error when I use the example files. I noticed, that the wd is ~/Desktop/a5_miseq_linux_20160825/bin and it searches for ../assembly_test_out.pp.bwt. But the file is in /bin
-
I also get the error when I use the example files
-
Error: could not open ../assembly.out.pp.bwt for read
-
Anonymous modified a comment on ticket #11
Originally posted by: hiren.gh...@gmail.com Reported by hiren.ghosh@gmail.com I am also getting same error. I am using illumina pair end read: [a5] Begin: 8:51 on 10-1-2013 [a5] Found the following libraries: raw1: id=raw1 p1=ResetH10_S1_L001_R1_001.fastq p2=ResetH10_S1_L001_R2_001.fastq [a5] Found 1 libraries [a5] Starting pipeline at step 1 [a5] Cleaning reads with SGA [a5] Cleaning reads with SGA preprocess: WARNING - it is suggested that the min read length is 40 preprocess: Using very short...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64 routine. You should open up the a5_pipeline.pl file, and change this subroutine; a couple other users have posted fixes here: https://code.google.com/p/ngopt/issues/detail?id=5
-
Anonymous modified a comment on ticket #11
Originally posted by: hiren.gh...@gmail.com Reported by hiren.ghosh@gmail.com I am also getting same error. I am using illumina pair end read: [a5] Begin: 8:51 on 10-1-2013 [a5] Found the following libraries: raw1: id=raw1 p1=ResetH10_S1_L001_R1_001.fastq p2=ResetH10_S1_L001_R2_001.fastq [a5] Found 1 libraries [a5] Starting pipeline at step 1 [a5] Cleaning reads with SGA [a5] Cleaning reads with SGA preprocess: WARNING - it is suggested that the min read length is 40 preprocess: Using very short...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64 routine. You should open up the a5_pipeline.pl file, and change this subroutine; a couple other users have posted fixes here: https://code.google.com/p/ngopt/issues/detail?id=5
-
RUBENS DANIEL MISERANI MAGALHAES posted a comment on ticket #20
Please, any news about this ticket. I have the same problem here.
-
Santiago created ticket #23
Unpaired reads are not being used
-
Sam Hong created ticket #22
Assembly returns error, says reads are unpaired when they are
-
ngopt released /a5_miseq_linux_20160825.tar.gz
-
-
Aaron Darling committed [r870]
Check for a supported output path and provide a...
-
support test of assemblies without scaffolding
-
don't polish metagenome assemblies
-
This is likely to be a problem specific to your cluster. Check the CPU architecture...
-
Sébastien created ticket #21
Permission denied when using A5 for MiSeq on university supercomputer
-
Bernardo Bello Orti modified a comment on a wiki page
Test run of A5 unsuccessful. How is that possible? -sh-4.1$ pwd /home/bernardo/a5_miseq_linux_20150522...
-
Test run of A5 unsuccessful. How is that possible? -sh-4.1$ pwd /home/bernardo/a5_miseq_linux_20150522...
-
Segmentation fault (finally worked with just one thread) Could we fix that? [a5]...
-
Luca modified a comment on ticket #18
Hello! First of all thanks a lot for this amazing software. We have experienced some...
-
Hello! First of all thanks a lot for this amazing software. We have experienced some...
-
Hi Aaron, I have missed this email and found it today. I'm attaching the first 10...
-
Jean-Guillaume E-R posted a comment on ticket #16
Hi, did you find a way to resolve this error message? I had the same problem as ...
-
Thanks for the log, Santiago. It looks like there was a problem parsing the assembly...
-
Error "Modification of non-creatable array value attempted"
-
hmontenegro modified a comment on ticket #19
I was getting these same errors as well, but in the end it turned out I was inputing...
-
I was geting these same errors as well, but in the end it turned out I was inputing...
-
I was geting these same errors as well, but in the end it turned out I was inputing...
-
Karsten Liere posted a comment on ticket #19
Hi, well I tried the latest A5 version 20150522, however, IDBA is still crashing,...
-
-
-
make java heap size explicit to workaround glit...
-
update java link to the JDK
-
sh: line 1: 4952 Segmentation fault: 11
-
changes to (1) fix java check on OS X yosemite ...
-
Hi Aaron, do you have any news about this? Thanks.
-
Hi Aaron, I'm using the latest version, a5pipeline-20141120.
-
skip SSPACE scaffolding by default since it see...
-
Hi Santiago, can you please let us know exactly which version of A5 your are using?...
-
Errors on the A5qc.jar command
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Hi Julian, these are big questions about sequencing strategy. You're better off asking...
-
<REDACTED> modified a comment on ticket #17
Sorry to bother that much mr Darling, your hints are helping me very much at that...
-
<REDACTED> posted a comment on ticket #17
Sorry to bother that much mr Darling, your help is very helping me at that moment..!...
-
-
-
ok, your best bet is to check out the latest source code (important bugfixes), and...
-
<REDACTED> posted a comment on ticket #17
Thanks for the answer! Yes its bacterial genome, but the fact is that I did not want...
-
Hi Julian, you are probably using A5-miseq if the pipeline made it to the A5qc step...
-
create split read 1 & read 2 files for each cor...
-
<REDACTED> created ticket #17
Error in detecting missasemblies
-
restoring conditional AGP production (at David ...
-
improve behavior on pathological datasets such ...
-
improved error reporting when read pairs not found
-
add %GC to stats file
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
Anonymous modified a comment on a wiki page
Originally posted by: rohan.ma...@gmail.com This is due to a bug in the get_phred64...
-
unconditionally make AGP
-
Peter Hoyt posted a comment on ticket #16
I should mention that TrimmomaticSE completed successfully, with only 1% of the reads...
-
Can't find error corrected reads DDRxxxxxx.ec.fastq at /opt/ngopt/a5_miseq_linux_20140604/bin/a5_pipeline.pl line 253
-
-
-
clean up output and bugfix for sga threading on...
-
bugfix for case where region at end of contig h...
-
removing false alarm
-
not all SAM have a 12th column, apparently
-
-
-
fix for silly character escape bug, thanks to K...
-
-
-
-
-
-
-
-
-
-
-
-
-
permit IUPAC ambiguities
-
-
-
fix for A5QC bug with multiply-mapped reads, al...
-
A5PipelineREADME
-
-
-
-
-
-
some packaging adaptations for sourceforge
1 >
