Activity for Sergey Koren
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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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The error message is that you do not have sufficient coverage in corrected reads...
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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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This looks like an internal blasr error so restarting won’t likely fix it (the match...
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It sounds like your frg is incorrect or your data is bad. The frg file specifies...
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FastqToCA requires fastq input not fasta so you’ll have to add quality values so...
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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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Canu does not support any assembly using Illumina reads. It is designed for only...
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We plan on not supporting the entire WGS package. The relevant parts have been integrated...
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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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This behavior is correct when running on the grid. Once the job is submitted to the...
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use /usr/bin/env time instead of /usr/bin/time
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I looked through your asm.layout.err you posted earlier. It seems that either the...
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There is a file produced from the correction named <library name="">.log which gives...
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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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This means one of the overlap job output files is corrupt. Most likely one of the...
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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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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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Normally when using bash /usr/bin/time != time as /usr/bin/time is GNU Time and time...
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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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Assembling a MinION dataset - spec falcon_sense options problems
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Several users have had success with the SLURM patch on github so I would recommend...
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asm.spec file missing
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Yes, the file was removed because more recent version 8.2+ automatically launch runCA...
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Could not realloc memory error in smrtpipeline
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It looks like you're using an internal log file (asm.[0-9]*.log). There should be...
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Hi, The problem from the output looks like not all the files were removed before...
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It's hard to tell which folders/files were removed because the markup removes the...
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Did you try both my suggestions above without success? Remove 5-* and any greater...
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Hi, That is correct, the text parser removed a * from my reply. Each individual seqDB.v002.*...
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Hi, I think this is related to the assembler generating extra contigs for very repetitive...
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Hi, You can try re-computing consensus by following the steps above to remove the...
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Hi, You can try re-computing consensus by following the steps above to remove the...
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Hi, You can try re-computing consensus by following the steps above to remove the...
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This is most likely because the assembler was built with a newer GCC (4.8.3) than...
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Only version 8.3rc2 has the added support for the falcon options required for nanopore...
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Error: found output from runCorrection. Stopping to avoid infinite loops. To try again, remove asm.layout.*
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Yes, that is correct, you have to remove runCorrection.sh as well as asm.layout.*....
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Update error message when runCorrection.sh fails
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Restoring commit erased by SourceForge's FS fai...
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The spec file specifies not to use the grid (useGrid=0 scriptOnGrid=0). I'm not sure...
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As I suspected, it is running 31 jobs on your node (and not using the grid which...
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The issue is not Celera Assembler by the resources SMRTportal is requesting for the...
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The issue is not Celera Assembler by the resources SMRTportal is requesting for the...
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The issue is not Celera Assembler by the resources SMRTportal is requesting for the...
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Hi, I replied to your previous email from June. Basically, if there is no short read...
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issue compiling 8.3rc2
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PBcR wgs 8.3rc2 versus 8.2 different overlapper behavior
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Fix is committed to repo.
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fix propagation of auto-detected parameters to ...
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I've seen some instability in PBDAGCON on various systems because of it's static...
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I've found the issue and will commit a fix. There is a subset of parameters that...
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There was a user at Rutgers who was looking into this as well and was planning to...
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This is part of the kmer package which is required to build CA and included in the...
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You are missing the python-dev package which includes python.h. you can either install...
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To clarify, Brian is talking about the runCA default which is set to 2 threads. PBcR...
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This does sound like a bug. Does your spec file specify anything for threads (ovlThreads,...
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I left it running and forgot about it and checked it this week and saw it was finished....
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My assembly and correction finished last week so I can post both the corrected reads...
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I was going to say something similar to Brian. The asm.tigStore is versioned so each...
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The rm -r 5-consensus- is missing a wildcard on the end, it should be rm -r 5-consensus-*....
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You have to follow the steps I listed to remove the 5-consensus/consensus.success...
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I've seen some rare cases with large contigs (i.e. > 35Mbp) where the PacBio unitig...
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I've seen some rare cases with large contigs (i.e. > 35Mbp) where the PacBio unitig...
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The error looks like the cluster configuration is pointing to a different lib version...
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Based on the output the overlapper was submitted to the grid: qsub -q jje,free64,pub64,abio,bio...
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Based on the output the overlapper was submitted to the grid: qsub -q jje,free64,pub64,abio,bio...
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I verified the grid submission with local staging works on our local system so I...
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It looks like the JVM was trying to reserve 70GB of ram but your machine didn't actually...
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I can confirm that my run with the default mer worked and I have over 25X of corrected...
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Hi, Is this a new run or resuming an existing one? What is your command line and...
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Hi, I think I've identified the issue. Your spec file specifies: merSize=22 which...
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Cannot get fastqToCA to run
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It is possible to install and run a 32-bit version of the OS on a 64-bit processor....
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Remove hard-coded asm coverage in file check
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Fix restarting with existing corrected reads
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Sigh, some more PBS issues
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fix PBS identifier in runCA as well
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Fix PBS array job ID
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I was able to download the data and launch a run. From all the output files you sent,...
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Ah, that's the issue, you have a 32-bit system which is unsupported. The assembler...
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Most likely, the pre-compiled Linux binaries are not compatible with your system....
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overlapper jobs failed
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Linking bug in MaSuRCA installation, not related to Celera Assembler.
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Yes, that error implies something is wrong in your compilation/installation of MaSuRCA...
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The system resources for overlapping (memory and cores) are configured through runCA:...
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It looks like you're running MaSuRCA. MaSuRCA uses a fork of an older version of...
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It looks like you're running MaSuRCA. MaSuRCA uses a fork of an older version of...
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It looks from the gatekeeper and overlap outputs that your fragments were properly...
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It looks from the asm.layout.err file that the coverage based on overlaps is very...
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Hi, The likeliest reason is an empty input fastq file. Can you check the size of...
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First, you can definitely erase 0-overlaptrim/*Store folders to free up space since...
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