AMOS / Bugs / #29 casm-layout ERROR

ddsommer - 2020-04-25

How are you running "concensus" if the casm-layout program had already
failed to produce the CTG bank files? What was the error or log from
casm-layout?

On Wed, Apr 15, 2020 at 10:37 AM Francesco Cicconardi francicco@users.sourceforge.net wrote:

Unfortunately casm-layout:

casm-layout -t 1000 -U ${supercontigs}.layout -C ${supercontigs}.conflict
-b ${supercontigs}.bnk ${supercontigs}.delta

fails to generate the some files, specifically CTG.0.map, CTG.0.0.fix and
CTG.0.0.var

I get the following error when trying to run the consensus:

Entering 'Amos_supercontigs.bnk'Found CTG bank
unlocking 'r 432968 tk19812'Found FRG bankFound LAY bankFound LIB bankFound RED bankFound SCF bankFound UNV bank
IFOs found: 7File locks: 0Bank locks: 1

Starting on Wed Apr 15 14:49:31 2020
Read bank is Amos_supercontigs.bnkAlignment error rate is 0.06Minimum overlap bases is 10Output will be written to the bank AMOS Exception WHAT: Invalid Header, Map file is corrupted for Amos_supercontigs.bnk/CTG.0.mapLINE: 511FILE: IDMap_AMOS.cc

Why is that, I whould have anough memory.

Thanks a lot
Francesco

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- Francesco Cicconardi - 2020-04-25
  
  Hi,
  
  I think consensus fails because layout didn't generate the file. layout also finishes without error messages
  
  Thanks a lot
  F
  
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  - ddsommer - 2020-04-25
    
    Yes that is correct it is failing because of the missing CTG files. Is
    there a amos log file with logging from the casm-layout step?
    
    On Sat, Apr 25, 2020 at 12:34 PM Francesco Cicconardi francicco@users.sourceforge.net wrote:
    
    Hi,
    
    I think consensus fails because layout didn't generate the file. layout
    also finishes without error messages
    
    Thanks a lot
    
    F
    
    [bugs:#29] https://sourceforge.net/p/amos/bugs/29/ casm-layout ERROR*
    
    Status: open
    Group: v1.x.x
    Created: Wed Apr 15, 2020 02:37 PM UTC by Francesco Cicconardi
    Last Updated: Wed Apr 15, 2020 02:37 PM UTC
    Owner: nobody
    
    Hi,
    
    I'm trying to run AMOS, specifically casm-layout on a 33Gb delta file
    generated with nucmer. It took several days (> 14) to produce the delta
    file. Unfortunately casm-layout:
    
    casm-layout -t 1000 -U ${supercontigs}.layout -C ${supercontigs}.conflict
    -b ${supercontigs}.bnk ${supercontigs}.delta
    
    fails to generate the some files, specifically CTG.0.map, CTG.0.0.fix and
    CTG.0.0.var
    
    I get the following error when trying to run the consensus:
    
    Entering 'Amos_supercontigs.bnk'Found CTG bank
    unlocking 'r 432968 tk19812'Found FRG bankFound LAY bankFound LIB bankFound RED bankFound SCF bankFound UNV bank
    IFOs found: 7File locks: 0Bank locks: 1
    
    Starting on Wed Apr 15 14:49:31 2020
    Read bank is Amos_supercontigs.bnkAlignment error rate is 0.06Minimum overlap bases is 10Output will be written to the bank AMOS Exception WHAT: Invalid Header, Map file is corrupted for Amos_supercontigs.bnk/CTG.0.mapLINE: 511FILE: IDMap_AMOS.cc
    
    Why is that, I whould have anough memory.
    
    Thanks a lot
    Francesco
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/amos/bugs/29/
    
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    Related
    
    Bugs: #29
    
    alternate
    
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    - Francesco Cicconardi - 2020-04-25
      
      Now I don't have it anymore, but the log file was just listing the different stages of the job like:
      INPUT
      reads
      lis
      ...
      till the end without returning any expicit error.
      
      F
      
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      - Francesco Cicconardi - 2020-04-26
        
        I'm suspecting it's a memory issue. Is there any chance I can split the delta file to run part of that and reconnect them after?
        
        Cheers
        F
        
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    - Francesco Cicconardi - 2020-04-26
      
      Hi,
      
      This is the new log.
      
      ESC[0;35m###### Wed Apr 22 05:43:48 BST 2020: Running layoutESC[0m
      INPUT
      reads
      lis
      mates
      PLACEMENT
      CONFLICT
      ASSEMBLY
      OUTPUT
      ESC[0;35m###### Sun Apr 26 17:18:38 BST 2020: Running consensusESC[0m
      Entering 'Amos_supercontigs.bnk'
      Found CTG bank
      unlocking 'r 432968 tk19812'
      Found FRG bank
      Found LAY bank
      Found LIB bank
      Found RED bank
      Found SCF bank
      Found UNV bank
      
      IFOs found: 7
      File locks: 0
      Bank locks: 1
      
      Starting on Sun Apr 26 17:18:38 2020
      
      Read bank is Amos_supercontigs.bnk
      Alignment error rate is 0.06
      Minimum overlap bases is 10
      Output will be written to the bank
      AMOS Exception
      WHAT: Invalid Header, Map file is corrupted for Amos_supercontigs.bnk/CTG.0.map
      LINE: 511
      FILE: IDMap_AMOS.cc
      
      Cheers
      F
      
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