Activity for Whole-Genome Shotgun Assembler
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Ling Jin created ticket #342
overlapStoreBuild failed
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lpryszcz posted a comment on ticket #261
Thanks Sergey, it did the trick! https://github.com/alekseyzimin/masurca/issues/8#issuecomment-374885969 Any idea why the error occured? Greetings from Waw! L. L. On 20 March 2018 at 17:37, Sergey Koren skoren@users.sourceforge.net wrote: CA support ended in 2016. You should contact the MaSuRCA support team instead. Are you specifying doFragmentCorrection=0 in the MaSuRCA config? That is not going to work, it's a CA option not a MaSuRCA option. You need to run the CA command MaSuRCA is running but...
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Sergey Koren posted a comment on ticket #261
CA support ended in 2016. You should contact the MaSuRCA support team instead. Are you specifying doFragmentCorrection=0 in the MaSuRCA config? That is not going to work, it's a CA option not a MaSuRCA option. You need to run the CA command MaSuRCA is running but with the added parameter.
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Hi, I'm having similar issue in v2.3.4 and unfortunately your tweak doFragmentCorrection=0 doesn't work:/ Any other solutions? Error line 55 of configuration file 'configuration.txt': Invalid line 'doFragmentCorrection=0'
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Fuyou Fu posted a comment on ticket #341
OK. Thanks. Fuyou On Fri, Dec 16, 2016 at 7:51 AM, Sergey Koren skoren@users.sf.net...
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The error message is that you do not have sufficient coverage in corrected reads...
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runCA error!
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20X coverage is the minimum recommended for Canu so you can give it a shot with the...
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Seigfried posted a comment on ticket #32
Hello Sergey 'This looks like an internal blasr error so restarting won’t likely...
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This looks like an internal blasr error so restarting won’t likely fix it (the match...
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PBCR blasr failure
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Anonymous modified a comment on ticket #140
I just submitted this on a new thread because I feel like it's a completely different...
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Bright created ticket #31
How to configure on a grid system
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I had solved this problem using the parameter "-V" (sed -i 's#qsub#qsub -V' PBcR)....
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This problm occur when I submit job to SGE, run in local wouldn't make trouble. It...
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runCorrection failed as `GOMP_4.0' not found
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SamToCA conversion failed
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wangyugui posted a comment on ticket #339
I tried kmer 31 and overlap size 60, and there still have Reading layouts from '/biowrk/celera/juglans.regian/PRJNA291087.DNA/5-consensus/juglans.fixes'....
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Cannot determine type of file '.gkpStore:untrim'. Tried
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the dirty fix seems work. please close this ticket.
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my friend give a dirty fix. i will test it. ``` Index: bin/caqc.pl --- bin/caqc.pl...
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my friend give a dirty fix. i will test it. Index: bin/caqc.pl --- bin/caqc.pl (revision...
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and the sort in terminator will use 1279m or more time, so we need to improve the...
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sort with multiple thread support to improve performance
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I'm sorry that it is so late to update this info. When I changed the kmer to 31 and...
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I haved remove Line 1142, and change other parm, it will take about 1 week to fi...
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Brian Walenz posted a comment on ticket #339
Hopefully you have some experience editing source code and compiling and etc. In...
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8 of 124 job failed with the same error. and the max memory usages is less than ...
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It sounds like your frg is incorrect or your data is bad. The frg file specifies...
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lamiaa lahlou posted a comment on ticket #340
thank you i trid it but i have another error . GKP finished with 1828231 alerts or...
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Do you have SGE installed? If no, leave out "useGrid=1 scriptOnGrid=1". If yes, ask...
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runCa error
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the server have 768G memory ,36 cnsConcurrency, and other cns default option, so...
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the right source Revision: 4656
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utgcnsfix failed
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medhat posted a comment on ticket #28
Thanks a lot for answering, According to what you said; First I need to do: java...
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FastqToCA requires fastq input not fasta so you’ll have to add quality values so...
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fastqToCA -l PacBio -s corrected_pacBio_seq.fasta > new.frg There is no need to -q...
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Yes, you’d have to first convert it to a frg format using fastqToCA. However, I’d...
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use Celera Assembler with corrected PacBio reads
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Canu does not support any assembly using Illumina reads. It is designed for only...
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yasir s created ticket #27
wgs/canu/recommendation
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We plan on not supporting the entire WGS package. The relevant parts have been integrated...
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Alex Bod posted a comment on ticket #338
Thanks, I switched to canu now and obtained assemblies on grid engies slurn and sge...
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We're not maintaining this anymore, and trying to not provide support, sorry. If...
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Luohao Xu posted a comment on ticket #334
So I took only 25X corrected reads, and changed some options such as ovlHashBlockLength...
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If no jobs are running when you check qsub, then it may have completed with an error,...
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Hello Sergey, Thanks for your reply. Tough, when trying to view the running jobs...
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Hello Sergey, Thanks for your reply. Tough, when trying to view the running jobs...
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This behavior is correct when running on the grid. Once the job is submitted to the...
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PBcR pipeline stops on grid engine without errors
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use /usr/bin/env time instead of /usr/bin/time
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Whole-Genome Shotgun Assembler released /wgs-assembler/wgs-8.3/wgs-8.3rc2-Darwin_amd64.tar.bz2
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shichengcheng posted a comment on ticket #337
Many thanks! I firstly checked the input data, and the bases number of PacBio data...
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I looked through your asm.layout.err you posted earlier. It seems that either the...
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Hi, I changed the merSize to 16 and re-runed the pipeline,but it seems that the merSize...
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There is a file produced from the correction named <library name="">.log which gives...
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Christophe Klopp created ticket #25
PBcR MHAP / Correspondance input and corrected reads
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Marcela Uliano da Silva posted a comment on ticket #335
Hey Brian, my job finished! Thanks for your help! So, as an estimation: 1 million...
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Hi Brian! Thanks a lot for your answer. Ok, I understand your point. I've been, in...
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Hi Brian! Thanks a lot for your answer. Ok, I understand your point. I've been, in...
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Thanks a lot for your kind reply!!! I will add data to 20X+ and change the merSize...
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Generally 50X of a human genome requires 2-4TB to complete. However, this will vary...
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Too large output when running runCorrection.sh
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Too large output when running runCorrection.sh
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Too large output when running runCorrection.sh
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That doesn't look like a memory error, but I'm not sure why it failed. It's just...
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I'm attaching here my meryl.err file, it really seems like a memory error, right?...
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Run PBcR meryl failure
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Mahul Chakraborty posted a comment on ticket #333
Thanks for the suggestion, Sergey. Yes, this happened during the correction stage.....
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This means one of the overlap job output files is corrupt. Most likely one of the...
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'Segmentation fault' during 8-consensus
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Assertion `bof->bufferPos <= bof->bufferLen' failed
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George Sun posted a comment on ticket #331
Yeah, I agree. /usr/bin/env time should be better. Would you consider to change the...
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Jessica Hill posted a comment on ticket #24
After looking at the QVs more and doing some research, I came across some changes...
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I don't see anything odd when I run fastqAnalyze -stats. I'm attaching a file with...
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I don't see anything odd when I run fastqAnalyze -stats. I'm attaching a file with...
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Yes, it should be 237. Unfortunately if a read is not in the log you cannot easily...
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Yes, it should be 237. Unfortunately if a read is not in the layout you cannot easily...
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Typically a human-sized genome requires 2-4TB of space to run. It can be higher for...
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Peng Tian created ticket #332
asm.layout.err in corretion process
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I see. I will try it after the holiday.
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I meant that running "time" would report different results so it wouldn't keep the...
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I meant that running "time" would report different results so it wouldn't keep the...
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Yeah, I replaced them by "time" in the patch I provided. Are you suggesting me to...
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Normally when using bash /usr/bin/time != time as /usr/bin/time is GNU Time and time...
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PBcR: hard-coded absolute path to `time`
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I have, once, seen an Illumina file that had a QV one higher than the spec allowed....
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Genome assemly by PBcR
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I have 50X pacbio data. I want to assemly a genome near 1GB. Our system have 300...
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Invalid QVs
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Now It is clear, but I think the end should be 689 + 237 = 926 instead of 689 + 227...
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I am Using the right file as sugested from documentation in such case it is ecoli_assembly.log...
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Ah, OK I was confused since the reads were so split up which is surprising and seems...
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wgs 8.3 compilation error
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PBCR reads split after error correction
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