[Chromaseqlist] ACE file contains no contigs!

michele hoffman mhoffman.az at gmail.com
Wed Jun 29 19:04:45 PDT 2011 

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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