[Chromaseqlist] ACE file contains no contigs!

David Maddison david.maddison at science.oregonstate.edu
Wed Jun 29 21:45:56 PDT 2011 

Michele,

Did you do anything at all in between the last time and worked and now?  Upgrade phred/phrap, update other software on your computer such as install a Java update?  What type of computer are you using?  Could you send (off list) the start of your log file?

Has anyone else seen this problem?

Best wishes,
David

On 29 Jun  2011, at 7:04 PM, michele hoffman wrote:

> Hi all, 
> I had this module running great and all of a sudden I am seeing this error.  Here is the output using David's test file.
> Thank you for helping.  Happy Canada Day!
> 
> Michele Hoffman PhD 
> USDA ARS 
> 
> 
> 
> Problem running Chromaseq:
> 
> 
> Arguments:  [ -mqex ]
> Loading manual for searching..... manual ready.
> Segregate Chromatograms > extract
> 
> (Choose rule describing file name structure) # 
> (Mesquite) # Process Chromatograms > processChromatograms
> 
> (Phred/Phrap/Chromaseq Options) # 
> (Phred Phrap Locations & Options) # 
> (Mesquite) # 
> (Mesquite) # 
> (File Dialog: Choose directory containing ABI files: (/Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms2)) # 
> (Mesquite) # Process Chromatograms > processChromatograms
> 
> (Phred/Phrap/Chromaseq Options) # 
> (Mesquite) # 
> (File Dialog: Choose directory containing ABI files: (/Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms2)) # 
> (Mesquite) # 
> Phred Phrap processing of chromatograms as scripted by Mesquite
>  Processing directory: 
>   /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms
> 
> Using primers file: /Users/mhoffman/phredphrap/Primers.txt
> 
> Parameters: Phred Options:  -id . -pd . -d 
> Phrap Options:  -new_ace -qual_show 20 -vector_bound 0 
> Chromaseq Options: 
>     Quality threshold for lower case: 49
>     Convert multiple-peaks sites to ambiguity codes: true
>     Minimum secondary peak fraction for ambiguity: 0.3
>     Trim low quality regions from ends: true
>     Quality threshold for trim: 20
>     Trim window length: 10
>     Trim window threshold: 5
> 
> 
> ---------------------------------------------------
> Section 1: Examining chromatogram files and preparing directories 
> 
>   Preparing DNA1120_B1490_411940 ab1  (COI)
>   Preparing DNA1120_Bcoi2R_412036 ab1  (COI)
>   Preparing DNA1250_B1490_208508 ab1  (COI)
>   Preparing DNA1250_B2232_208604 ab1  (COI)
>   Preparing DNA1250_D3aR_572645 ab1  (28S)
>   Preparing DNA1250_NLF184_572549 ab1  (28S)
>   Preparing DNA2320_D3aR_552091 ab1  (28S)
>   Preparing DNA2320_NLF184_551995 ab1  (28S)
>   Preparing DNA1856_B1490_237723 ab1  (COI)
>   Preparing DNA1856_B2232_237819 ab1  (COI)
>   Preparing DNA1120_D1_394061 ab1  (28S)
>   Preparing DNA1120_D3_394157 ab1  (28S)
>   Preparing DNA1856_D1_237563 ab1  (28S)
>   Preparing DNA1856_D3_237659 ab1  (28S)
> 
> Number of files prepared: 14
> 
> ---------------------------------------------------
> Section 2: Renaming chromatograms for Phred and Phrap
> 
>   A01_A01DNA1120_B1490_411940.ab1  renamed to  DNA1120_B1490_411940.b.B1490.ab1
>   A01_A01DNA1120_Bcoi2R_412036.ab1  renamed to  DNA1120_Bcoi2R_412036.g.Bcoi2R.ab1
>   C07_C07DNA1250_B1490_208508.ab1  renamed to  DNA1250_B1490_208508.b.B1490.ab1
>   C07_C07DNA1250_B2232_208604.ab1  renamed to  DNA1250_B2232_208604.g.B2232.ab1
>   C12_C12DNA1250_D3aR_572645.ab1  renamed to  DNA1250_D3aR_572645.g.D3aR.ab1
>   C12_C12DNA1250_NLF184_572549.ab1  renamed to  DNA1250_NLF184_572549.b.NLF184.ab1
>   F06_F06DNA2320_D3aR_552091.ab1  renamed to  DNA2320_D3aR_552091.g.D3aR.ab1
>   F06_F06DNA2320_NLF184_551995.ab1  renamed to  DNA2320_NLF184_551995.b.NLF184.ab1
>   H05_H05DNA1856_B1490_237723.ab1  renamed to  DNA1856_B1490_237723.b.B1490.ab1
>   H05_H05DNA1856_B2232_237819.ab1  renamed to  DNA1856_B2232_237819.g.B2232.ab1
>   H07_H07DNA1120_D1_394061.ab1  renamed to  DNA1120_D1_394061.b.D1.ab1
>   H07_H07DNA1120_D3_394157.ab1  renamed to  DNA1120_D3_394157.g.D3.ab1
>   H09_H09DNA1856_D1_237563.ab1  renamed to  DNA1856_D1_237563.b.D1.ab1
>   H09_H09DNA1856_D3_237659.ab1  renamed to  DNA1856_D3_237659.g.D3.ab1
> 
> 
> 
> ---------------------------------------------------
> Section 3: Execution of Phred-Phrap command file begun
> 
> ....1. DNA1120_B1490_411940 ab1 (Phred)
> 1. DNA1120_B1490_411940 ab1 (Phrap)
> 2. DNA1120_Bcoi2R_412036 ab1 (Phred)
> 2. DNA1120_Bcoi2R_412036 ab1 (Phrap)
> 3. DNA1250_B1490_208508 ab1 (Phred)
> 3. DNA1250_B1490_208508 ab1 (Phrap)
> 4. DNA1250_B2232_208604 ab1 (Phred)
> 4. DNA1250_B2232_208604 ab1 (Phrap)
> 5. DNA1250_D3aR_572645 ab1 (Phred)
> 5. DNA1250_D3aR_572645 ab1 (Phrap)
> 6. DNA1250_NLF184_572549 ab1 (Phred)
> 6. DNA1250_NLF184_572549 ab1 (Phrap)
> 7. DNA2320_D3aR_552091 ab1 (Phred)
> 7. DNA2320_D3aR_552091 ab1 (Phrap)
> 8. DNA2320_NLF184_551995 ab1 (Phred)
> 8. DNA2320_NLF184_551995 ab1 (Phrap)
> 9. DNA1856_B1490_237723 ab1 (Phred)
> 9. DNA1856_B1490_237723 ab1 (Phrap)
> 10. DNA1856_B2232_237819 ab1 (Phred)
> 10. DNA1856_B2232_237819 ab1 (Phrap)
> 11. DNA1120_D1_394061 ab1 (Phred)
> 11. DNA1120_D1_394061 ab1 (Phrap)
> 12. DNA1120_D3_394157 ab1 (Phred)
> 12. DNA1120_D3_394157 ab1 (Phrap)
> 13. DNA1856_D1_237563 ab1 (Phred)
> 13. DNA1856_D1_237563 ab1 (Phrap)
> 14. DNA1856_D3_237659 ab1 (Phred)
> 
> Phred & Phrap analyses completed.
> 
> ---------------------------------------------------
> Section 4: Mesquite processing of Phrap results
>  
> Processing ACE file: DNA1120_D1_394061 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1120_D1_394061 ab1/DNA1120_D1_394061 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1120_D3_394157 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1120_D3_394157 ab1/DNA1120_D3_394157 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1250_D3aR_572645 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1250_D3aR_572645 ab1/DNA1250_D3aR_572645 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1250_NLF184_572549 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1250_NLF184_572549 ab1/DNA1250_NLF184_572549 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1856_D1_237563 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1856_D1_237563 ab1/DNA1856_D1_237563 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1856_D3_237659 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA1856_D3_237659 ab1/DNA1856_D3_237659 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA2320_D3aR_552091 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA2320_D3aR_552091 ab1/DNA2320_D3aR_552091 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA2320_NLF184_551995 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/28S/sequences/DNA2320_NLF184_551995 ab1/DNA2320_NLF184_551995 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1120_B1490_411940 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1120_B1490_411940 ab1/DNA1120_B1490_411940 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1120_Bcoi2R_412036 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1120_Bcoi2R_412036 ab1/DNA1120_Bcoi2R_412036 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1250_B1490_208508 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1250_B1490_208508 ab1/DNA1250_B1490_208508 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1250_B2232_208604 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1250_B2232_208604 ab1/DNA1250_B2232_208604 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1856_B1490_237723 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1856_B1490_237723 ab1/DNA1856_B1490_237723 ab1m.ace
>    ACE file contains no contigs!
> Processing ACE file: DNA1856_B2232_237819 ab1.ace
> /Users/mhoffman/Desktop/ChromaseqExamples/Chromatograms/processed/COI/sequences/DNA1856_B2232_237819 ab1/DNA1856_B2232_237819 ab1m.ace
>    ACE file contains no contigs!
> 
> 
> ========================
> Section 5: Phred/Phrap processing report
> 
> Multi-read sequences FAILED to be obtained from the following genes and samples:
>        (28S) -- DNA1120_D1_394061 ab1
>        (28S) -- DNA1120_D3_394157 ab1
>        (28S) -- DNA1250_D3aR_572645 ab1
>        (28S) -- DNA1250_NLF184_572549 ab1
>        (28S) -- DNA1856_D1_237563 ab1
>        (28S) -- DNA1856_D3_237659 ab1
>        (28S) -- DNA2320_D3aR_552091 ab1
>        (28S) -- DNA2320_NLF184_551995 ab1
>        (COI) -- DNA1120_B1490_411940 ab1
>        (COI) -- DNA1120_Bcoi2R_412036 ab1
>        (COI) -- DNA1250_B1490_208508 ab1
>        (COI) -- DNA1250_B2232_208604 ab1
>        (COI) -- DNA1856_B1490_237723 ab1
>        (COI) -- DNA1856_B2232_237819 ab1
> 
> ========================
> 
> Processing of chromatogram files completed.
> 
> Mesquite > showPackageInfo "'/Applications/Mesquite_Folder/Mesquite.app/../mesquite/chromaseq/aChromaseqIntro//manual/index.html'"
> _______________________________________________
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---------------------------------
David R. Maddison
Department of Zoology
3029 Cordley Hall
Oregon State University
Corvallis, OR  97331   USA

david.maddison at science.oregonstate.edu

http://david.bembidion.org
http://mesquiteproject.org
http://macclade.org
http://tolweb.org

(541) 737 2834




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