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mapleforest / HaploMerger2

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Some nib files are missing! Die! #11

Open yanboANU opened 6 years ago

yanboANU commented 6 years ago

Hi, When I give canu's result to HaploMerger2, it can work. But when I give abruijn's result to HaploMerger2, it cannot work. And the error is following. The last line of _A2.axtChainRecipBestNet.log is: Some nib files are missing! Die!

Any advice would be helpful. Thanks.

mapleforest commented 6 years ago

Is it because you have too many scaffolds/contigs and low N50 sizes?

Can you look into the seq directory to see if all nib files (they are just seq files in the nib format) are there?

在 2017/11/29 13:37, yanboANU 写道:

Hi, When I give canu's result to HaploMerger2, it can work. But when I give abruijn's result to HaploMerger2, it cannot work. And the error is following. The last line of _A2.axtChainRecipBestNet.log is: Some nib files are missing! Die!

Any advice would be helpful. Thanks.

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yanboANU commented 6 years ago

Thanks for your reply. I find the reason, abruijn's output format is >circular_20_len:39672_cov:102. If two scaffolds have some cov, then produce two 102.nib, then HaploMerger2 didn't work.

Carol-Symbiomics commented 4 years ago

Hi, I'm a new user of Haplomerger2. Although I'm aware Haplomerger2 is not recommended for assemblies with N50 <50Kb, I want to use it for my assembly (done using DISCOVAR, N50 ~25Kb) to see if I can get a decent haploid reference assembly I'm trying to run each hm.batch script individually (following the suggested order). I've successfully run "hm.batchA1.initiation_and_all_lastz", yet when I've run the "hm.batchA2.chainNet_and_netToMaf" at the end of the log file "_A2.axtChainRecipBestNet.log" this appears Can't open Pver_lib4_filteredDiscovar_ScaffCsar_Gapfilled_ScaffSize_maskedx.seq/Scaffold_484_size225463.nib to read: No such file or directory However, I checked and the file Scaffold_484_size225463.nib is in fact in that directoty. Should I proceed with hm.batchA3.misjoin_processing? Why isn't that .nib file not found even though it is there?

Thanks for your help!

mapleforest commented 3 years ago

I know this is and old thread. To allow later people have a answer for this problem. I put this here:

If your raw diploid assembly has >2000 scaffold sequences, make sure to lift your system’s openable file handle limit by invocating “ulimit –n 655350” before running HM2!

There are more details about this in the manual.