Activity for Whole-Genome Shotgun Assembler

Ling Jin created ticket #342

Ling Jin — Tue, 07 Dec 2021 08:52:27 -0000

overlapStoreBuild failed

lpryszcz posted a comment on ticket #261

lpryszcz — Wed, 21 Mar 2018 10:15:34 -0000

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...

Sergey Koren posted a comment on ticket #261

Sergey Koren — Tue, 20 Mar 2018 16:37:30 -0000

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.

lpryszcz posted a comment on ticket #261

lpryszcz — Tue, 20 Mar 2018 16:25:57 -0000

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'

Fuyou Fu posted a comment on ticket #341

Fuyou Fu — Fri, 16 Dec 2016 16:36:34 -0000

OK. Thanks. Fuyou On Fri, Dec 16, 2016 at 7:51 AM, Sergey Koren skoren@users.sf.net...

Sergey Koren posted a comment on ticket #341

Sergey Koren — Fri, 16 Dec 2016 13:51:40 -0000

The error message is that you do not have sufficient coverage in corrected reads...

Fuyou Fu created ticket #341

Fuyou Fu — Fri, 16 Dec 2016 02:14:03 -0000

runCA error!

Sergey Koren posted a comment on ticket #32

Sergey Koren — Wed, 02 Nov 2016 13:57:35 -0000

20X coverage is the minimum recommended for Canu so you can give it a shot with the...

Seigfried posted a comment on ticket #32

Seigfried — Tue, 01 Nov 2016 02:43:54 -0000

Hello Sergey 'This looks like an internal blasr error so restarting won’t likely...

Sergey Koren posted a comment on ticket #32

Sergey Koren — Mon, 31 Oct 2016 21:03:27 -0000

This looks like an internal blasr error so restarting won’t likely fix it (the match...

Seigfried created ticket #32

Seigfried — Mon, 31 Oct 2016 05:45:38 -0000

PBCR blasr failure

Anonymous modified a comment on ticket #140

Anonymous — Sat, 17 Sep 2016 03:53:14 -0000

I just submitted this on a new thread because I feel like it's a completely different...

Bright created ticket #31

Bright — Wed, 24 Aug 2016 15:36:17 -0000

How to configure on a grid system

Bright posted a comment on ticket #30

Bright — Sun, 07 Aug 2016 12:19:58 -0000

I had solved this problem using the parameter "-V" (sed -i 's#qsub#qsub -V' PBcR)....

Bright posted a comment on ticket #30

Bright — Sun, 07 Aug 2016 09:44:27 -0000

This problm occur when I submit job to SGE, run in local wouldn't make trouble. It...

Bright created ticket #30

Bright — Sun, 07 Aug 2016 07:32:11 -0000

runCorrection failed as `GOMP_4.0' not found

Bright created ticket #29

Bright — Sun, 07 Aug 2016 06:02:43 -0000

SamToCA conversion failed

wangyugui posted a comment on ticket #339

wangyugui — Wed, 06 Jul 2016 09:39:27 -0000

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'....

wangyugui created ticket #142

wangyugui — Wed, 06 Jul 2016 06:49:58 -0000

Cannot determine type of file '.gkpStore:untrim'. Tried

wangyugui posted a comment on ticket #141

wangyugui — Wed, 06 Jul 2016 06:46:25 -0000

the dirty fix seems work. please close this ticket.

wangyugui modified a comment on ticket #141

wangyugui — Tue, 05 Jul 2016 11:04:14 -0000

my friend give a dirty fix. i will test it. ``` Index: bin/caqc.pl --- bin/caqc.pl...

wangyugui posted a comment on ticket #141

wangyugui — Tue, 05 Jul 2016 11:03:48 -0000

my friend give a dirty fix. i will test it. Index: bin/caqc.pl --- bin/caqc.pl (revision...

wangyugui posted a comment on ticket #141

wangyugui — Tue, 05 Jul 2016 09:25:30 -0000

and the sort in terminator will use 1279m or more time, so we need to improve the...

wangyugui created ticket #141

wangyugui — Tue, 05 Jul 2016 09:22:30 -0000

sort with multiple thread support to improve performance

wangyugui posted a comment on ticket #339

wangyugui — Tue, 21 Jun 2016 04:05:18 -0000

I'm sorry that it is so late to update this info. When I changed the kmer to 31 and...

wangyugui posted a comment on ticket #339

wangyugui — Fri, 06 May 2016 19:32:05 -0000

I haved remove Line 1142, and change other parm, it will take about 1 week to fi...

Brian Walenz posted a comment on ticket #339

Brian Walenz — Fri, 06 May 2016 18:24:39 -0000

Hopefully you have some experience editing source code and compiling and etc. In...

wangyugui posted a comment on ticket #339

wangyugui — Fri, 06 May 2016 17:51:03 -0000

8 of 124 job failed with the same error. and the max memory usages is less than ...

Sergey Koren posted a comment on ticket #340

Sergey Koren — Fri, 06 May 2016 13:58:18 -0000

It sounds like your frg is incorrect or your data is bad. The frg file specifies...

lamiaa lahlou posted a comment on ticket #340

lamiaa lahlou — Fri, 06 May 2016 10:49:32 -0000

thank you i trid it but i have another error . GKP finished with 1828231 alerts or...

Brian Walenz posted a comment on ticket #340

Brian Walenz — Fri, 06 May 2016 10:39:10 -0000

Do you have SGE installed? If no, leave out "useGrid=1 scriptOnGrid=1". If yes, ask...

lamiaa lahlou created ticket #340

lamiaa lahlou — Fri, 06 May 2016 09:23:48 -0000

runCa error

wangyugui posted a comment on ticket #339

wangyugui — Wed, 04 May 2016 02:09:36 -0000

the server have 768G memory ,36 cnsConcurrency, and other cns default option, so...

wangyugui posted a comment on ticket #339

wangyugui — Wed, 04 May 2016 01:25:41 -0000

the right source Revision: 4656

wangyugui created ticket #339

wangyugui — Wed, 04 May 2016 01:11:26 -0000

utgcnsfix failed

medhat posted a comment on ticket #28

medhat — Mon, 18 Apr 2016 13:55:27 -0000

Thanks a lot for answering, According to what you said; First I need to do: java...

Sergey Koren posted a comment on ticket #28

Sergey Koren — Sun, 17 Apr 2016 17:52:05 -0000

FastqToCA requires fastq input not fasta so you’ll have to add quality values so...

medhat posted a comment on ticket #28

medhat — Sat, 16 Apr 2016 08:39:16 -0000

fastqToCA -l PacBio -s corrected_pacBio_seq.fasta > new.frg There is no need to -q...

Sergey Koren posted a comment on ticket #28

Sergey Koren — Fri, 15 Apr 2016 13:13:35 -0000

Yes, you’d have to first convert it to a frg format using fastqToCA. However, I’d...

medhat created ticket #28

medhat — Fri, 15 Apr 2016 12:44:47 -0000

use Celera Assembler with corrected PacBio reads

Sergey Koren posted a comment on ticket #27

Sergey Koren — Thu, 24 Mar 2016 13:37:35 -0000

Canu does not support any assembly using Illumina reads. It is designed for only...

yasir s created ticket #27

yasir s — Wed, 23 Mar 2016 20:04:16 -0000

wgs/canu/recommendation

Sergey Koren posted a comment on ticket #338

Sergey Koren — Wed, 24 Feb 2016 17:07:51 -0000

We plan on not supporting the entire WGS package. The relevant parts have been integrated...

Alex Bod posted a comment on ticket #338

Alex Bod — Wed, 24 Feb 2016 13:56:02 -0000

Thanks, I switched to canu now and obtained assemblies on grid engies slurn and sge...

Brian Walenz posted a comment on ticket #334

Brian Walenz — Tue, 09 Feb 2016 20:09:59 -0000

We're not maintaining this anymore, and trying to not provide support, sorry. If...

Luohao Xu posted a comment on ticket #334

Luohao Xu — Tue, 09 Feb 2016 09:24:56 -0000

So I took only 25X corrected reads, and changed some options such as ovlHashBlockLength...

Sergey Koren posted a comment on ticket #338

Sergey Koren — Mon, 08 Feb 2016 21:09:46 -0000

If no jobs are running when you check qsub, then it may have completed with an error,...

Alex Bod modified a comment on ticket #338

Alex Bod — Tue, 02 Feb 2016 09:03:27 -0000

Alex Bod posted a comment on ticket #338

Alex Bod — Tue, 02 Feb 2016 09:03:04 -0000

Hello Sergey, Thanks for your reply. Tough, when trying to view the running jobs...

Alex Bod posted a comment on ticket #338

Alex Bod — Tue, 02 Feb 2016 09:02:40 -0000

Hello Sergey, Thanks for your reply. Tough, when trying to view the running jobs...

Sergey Koren posted a comment on ticket #338

Sergey Koren — Mon, 01 Feb 2016 18:45:08 -0000

This behavior is correct when running on the grid. Once the job is submitted to the...

Alex Bod created ticket #338

Alex Bod — Mon, 01 Feb 2016 10:55:00 -0000

PBcR pipeline stops on grid engine without errors

Sergey Koren committed [r4656]

Sergey Koren — Tue, 22 Dec 2015 14:17:16 -0000

use /usr/bin/env time instead of /usr/bin/time

Whole-Genome Shotgun Assembler released /wgs-assembler/wgs-8.3/wgs-8.3rc2-Darwin_amd64.tar.bz2

Whole-Genome Shotgun Assembler — Tue, 22 Dec 2015 14:04:02 -0000

shichengcheng posted a comment on ticket #337

shichengcheng — Mon, 14 Dec 2015 05:15:19 -0000

Many thanks! I firstly checked the input data, and the bases number of PacBio data...

Sergey Koren posted a comment on ticket #337

Sergey Koren — Mon, 14 Dec 2015 03:53:48 -0000

I looked through your asm.layout.err you posted earlier. It seems that either the...

shichengcheng posted a comment on ticket #337

shichengcheng — Mon, 14 Dec 2015 01:22:52 -0000

Hi, I changed the merSize to 16 and re-runed the pipeline,but it seems that the merSize...

Sergey Koren posted a comment on ticket #25

Sergey Koren — Fri, 11 Dec 2015 16:43:46 -0000

There is a file produced from the correction named .log which gives...

Christophe Klopp created ticket #25

Christophe Klopp — Fri, 11 Dec 2015 08:27:55 -0000

PBcR MHAP / Correspondance input and corrected reads

Marcela Uliano da Silva posted a comment on ticket #335

Marcela Uliano da Silva — Thu, 10 Dec 2015 13:08:52 -0000

Hey Brian, my job finished! Thanks for your help! So, as an estimation: 1 million...

Marcela Uliano da Silva posted a comment on ticket #335

Marcela Uliano da Silva — Wed, 09 Dec 2015 13:05:47 -0000

Hi Brian! Thanks a lot for your answer. Ok, I understand your point. I've been, in...

Marcela Uliano da Silva posted a comment on ticket #335

Marcela Uliano da Silva — Wed, 09 Dec 2015 12:44:49 -0000

Hi Brian! Thanks a lot for your answer. Ok, I understand your point. I've been, in...

shichengcheng posted a comment on ticket #337

shichengcheng — Wed, 09 Dec 2015 02:12:59 -0000

Thanks a lot for your kind reply!!! I will add data to 20X+ and change the merSize...

Sergey Koren posted a comment on ticket #337

Sergey Koren — Tue, 08 Dec 2015 18:29:44 -0000

Generally 50X of a human genome requires 2-4TB to complete. However, this will vary...

Sergey Koren modified ticket #336

Sergey Koren — Tue, 08 Dec 2015 18:28:01 -0000

Too large output when running runCorrection.sh

shichengcheng created ticket #337

shichengcheng — Tue, 08 Dec 2015 09:13:49 -0000

Too large output when running runCorrection.sh

shichengcheng created ticket #336

shichengcheng — Tue, 08 Dec 2015 09:12:14 -0000

Too large output when running runCorrection.sh

Brian Walenz posted a comment on ticket #335

Brian Walenz — Mon, 07 Dec 2015 17:56:09 -0000

That doesn't look like a memory error, but I'm not sure why it failed. It's just...

Marcela Uliano da Silva posted a comment on ticket #335

Marcela Uliano da Silva — Mon, 07 Dec 2015 14:19:21 -0000

I'm attaching here my meryl.err file, it really seems like a memory error, right?...

Marcela Uliano da Silva created ticket #335

Marcela Uliano da Silva — Mon, 07 Dec 2015 10:38:25 -0000

Run PBcR meryl failure

Mahul Chakraborty posted a comment on ticket #333

Mahul Chakraborty — Fri, 04 Dec 2015 20:00:32 -0000

Thanks for the suggestion, Sergey. Yes, this happened during the correction stage.....

Sergey Koren posted a comment on ticket #333

Sergey Koren — Fri, 04 Dec 2015 18:37:40 -0000

This means one of the overlap job output files is corrupt. Most likely one of the...

Luohao Xu created ticket #334

Luohao Xu — Fri, 04 Dec 2015 16:02:24 -0000

'Segmentation fault' during 8-consensus

Mahul Chakraborty created ticket #333

Mahul Chakraborty — Thu, 03 Dec 2015 09:45:13 -0000

Assertion `bof->bufferPos <= bof->bufferLen' failed

George Sun posted a comment on ticket #331

George Sun — Wed, 02 Dec 2015 16:18:36 -0000

Yeah, I agree. /usr/bin/env time should be better. Would you consider to change the...

Jessica Hill posted a comment on ticket #24

Jessica Hill — Mon, 30 Nov 2015 18:46:55 -0000

After looking at the QVs more and doing some research, I came across some changes...

Jessica Hill modified a comment on ticket #24

Jessica Hill — Mon, 30 Nov 2015 18:41:17 -0000

I don't see anything odd when I run fastqAnalyze -stats. I'm attaching a file with...

Jessica Hill posted a comment on ticket #24

Jessica Hill — Mon, 30 Nov 2015 16:06:38 -0000

I don't see anything odd when I run fastqAnalyze -stats. I'm attaching a file with...

Sergey Koren modified a comment on ticket #23

Sergey Koren — Fri, 27 Nov 2015 03:28:14 -0000

Yes, it should be 237. Unfortunately if a read is not in the log you cannot easily...

Sergey Koren posted a comment on ticket #23

Sergey Koren — Fri, 27 Nov 2015 03:27:52 -0000

Yes, it should be 237. Unfortunately if a read is not in the layout you cannot easily...

Sergey Koren posted a comment on ticket #332

Sergey Koren — Fri, 27 Nov 2015 03:25:46 -0000

Typically a human-sized genome requires 2-4TB of space to run. It can be higher for...

Peng Tian created ticket #332

Peng Tian — Fri, 27 Nov 2015 01:21:45 -0000

asm.layout.err in corretion process

George Sun posted a comment on ticket #331

George Sun — Wed, 25 Nov 2015 21:52:26 -0000

I see. I will try it after the holiday.

Sergey Koren modified a comment on ticket #331

Sergey Koren — Wed, 25 Nov 2015 21:06:40 -0000

I meant that running "time" would report different results so it wouldn't keep the...

Sergey Koren posted a comment on ticket #331

Sergey Koren — Wed, 25 Nov 2015 21:06:18 -0000

I meant that running "time" would report different results so it wouldn't keep the...

George Sun posted a comment on ticket #331

George Sun — Wed, 25 Nov 2015 20:51:11 -0000

Yeah, I replaced them by "time" in the patch I provided. Are you suggesting me to...

Sergey Koren posted a comment on ticket #331

Sergey Koren — Wed, 25 Nov 2015 20:42:18 -0000

Normally when using bash /usr/bin/time != time as /usr/bin/time is GNU Time and time...

George Sun created ticket #331

George Sun — Wed, 25 Nov 2015 16:03:50 -0000

PBcR: hard-coded absolute path to `time`

Brian Walenz posted a comment on ticket #24

Brian Walenz — Wed, 25 Nov 2015 14:47:02 -0000

I have, once, seen an Illumina file that had a QV one higher than the spec allowed....

Peng Tian created ticket #330

Peng Tian — Wed, 25 Nov 2015 09:17:32 -0000

Genome assemly by PBcR

Peng Tian posted a comment on ticket #311

Peng Tian — Wed, 25 Nov 2015 09:03:31 -0000

I have 50X pacbio data. I want to assemly a genome near 1GB. Our system have 300...

Jessica Hill created ticket #24

Jessica Hill — Tue, 24 Nov 2015 20:21:25 -0000

Invalid QVs

medhat posted a comment on ticket #23

medhat — Mon, 23 Nov 2015 11:32:05 -0000

Now It is clear, but I think the end should be 689 + 237 = 926 instead of 689 + 227...

medhat modified a comment on ticket #23

medhat — Mon, 23 Nov 2015 08:56:21 -0000

I am Using the right file as sugested from documentation in such case it is ecoli_assembly.log...

Sergey Koren posted a comment on ticket #23

Sergey Koren — Mon, 16 Nov 2015 20:18:15 -0000

Ah, OK I was confused since the reads were so split up which is surprising and seems...

Sergey Koren modified ticket #310

Sergey Koren — Mon, 16 Nov 2015 20:09:38 -0000

wgs 8.3 compilation error

Sergey Koren modified ticket #21

Sergey Koren — Mon, 16 Nov 2015 20:07:37 -0000

PBCR reads split after error correction