Unknown chemistry error

Charles Alexander songsponge at yahoo.com
Mon Aug 25 14:36:52 EST 2003


Hi folks,

Our sequencing facility recently upgraded to BigDye 3.1 on their ABI
3700 sequencer and now sequence reads seem to bomb in the phredPhrap
script with the "unknown chemistry" error.

I've looked thru our phredpar.dat file and there isn't anything
obvious popping out at me that looks amiss.  Here is an excerpt.
Things worked in 3.0  Anything else I should watch out for in making
sure our phred/phrap suite doesn't choke ?

Also, some files are coming up with the "unknown file type" error.
What could some probable causes of this error be ?

We're running phred/phrap/consed on a Sun Solaris.  Versions are:

phred version: 0.020425.c

phrap version 0.990329

POLYPHRED  Version 4.06

consed Version 13.0 (030423)

Thanks in advance,

Charles Alexander
----

"DP3700POP5_ET_v2.mob"          primer          energy-transfer
 ABI_3700
"DP3700POP5{BD-21M13}v1.mob"    primer          big-dye
 ABI_3700
"DP3700POP5{BD-M13Rev}v1.mob"   primer          big-dye
 ABI_3700
"DP3700POP6{BD-M13Rev}v1.mob"   primer          big-dye
 ABI_3700
"DP3700POP6{BD-21M13}v3.mob"    primer          big-dye
 ABI_3700
"DP3700POP6{BD-M13Rev}v2.mob"   primer          big-dye
 ABI_3700
"DP3100POP6{BD-21M13}v1.mob"    primer          big-dye
 ABI_3100
"DP3100POP6{BD-M13Rev}v1.mob"   primer          big-dye
 ABI_3100

...

"DT3700POP5{BD}v1.mob"          terminator      big-dye
 ABI_3700
"DT3700POP6{BD-MIT}v1.mob"      terminator      big-dye
 ABI_3700
"DT3700POP5{BD}v2.mob"          terminator      big-dye
 ABI_3700
"DT3700POP5{BD}v3.mob"          terminator      big-dye
 ABI_3700
"DT3700POP6{BD}v0_3.mob"        terminator      big-dye
 ABI_3700
"DT3700POP6{BD}v4.mob"          terminator      big-dye
 ABI_3700
"DT3700POP6{BD}v5.mob"          terminator      big-dye
 ABI_3700
"DT3700PO.MOB"                  terminator      big-dye
 ABI_3700
"DT3700POP6{37C}.mob"           terminator      big-dye
 ABI_3700
"DT3700POP6{BD-40deg}v1.mob"    terminator      big-dye
 ABI_3700
"DT3700FSP{BD}v1.mob"           terminator      big-dye
 ABI_3700
"DT3700POP5{dRhod}v1.mob"       terminator      d-rhodamine
 ABI_3700
"DT3700POP6{dRhod}v3.mob"       terminator      d-rhodamine
 ABI_3700
"DT3700POP5{ET}.mob"            terminator      energy-transfer
 ABI_3700
"DT3100POP6{dRhod}v1.mob"       terminator      d-rhodamine
 ABI_3100
"DT3100POP6{BD}v2.mob"          terminator      big-dye
 ABI_3100
"DT3100POP6{BDv3}v1.mob"        terminator      big-dye
 ABI_3100
---




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