Hi,
I have not had much success converting a 454 ace file to bnk and viewing it on hawkeye. Here are the errors I get during conversion:
any insight into this will be appreciated.
Thanks
[mukatira@sjmemmps02 NEXTGEN_SEQ]$ toAmos -ace chrM.ace -o - |bank-transact -m - -b chrM.bnk -c
START DATE: Tue Jul 29 09:34:53 2008
Bank is: chrM.bnk
Reading messages from standard in
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:4, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:6, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:8, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:9, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:10, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:44, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:45, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:46, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:50, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:52, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:54, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:56, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'CTG' message with iid:1, message ignored
Messages read: 117
Objects added: 104
Objects deleted: 0
Objects replaced: 0
END DATE: Tue Jul 29 09:34:53 2008
[mukatira@sjmemmps02 NEXTGEN_SEQ]$ hawkeye chrM.bnk/
Opening chrM.bnk/... ERROR in openBank():
WHAT: Could not open bank file, chrM.bnk//CTG.ifo, No such file or directory
LINE: 1037
FILE: Bank_AMOS.cc
Segmentation fault
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
Could you please post an example sequence and quality record from the .ace file? Hawkeye is complaining because either the consensus quality values are missing, or there is a mismatch between the number of bases in the consensus and the number of quality values.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I have not had much success converting a 454 ace file to bnk and viewing it on hawkeye. Here are the errors I get during conversion:
any insight into this will be appreciated.
Thanks
[mukatira@sjmemmps02 NEXTGEN_SEQ]$ toAmos -ace chrM.ace -o - |bank-transact -m - -b chrM.bnk -c
START DATE: Tue Jul 29 09:34:53 2008
Bank is: chrM.bnk
Reading messages from standard in
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:4, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:6, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:8, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:9, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:10, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:44, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:45, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:46, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:50, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:52, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:54, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'RED' message with iid:56, message ignored
ERROR: Sequence and quality lengths disagree
could not parse 'CTG' message with iid:1, message ignored
Messages read: 117
Objects added: 104
Objects deleted: 0
Objects replaced: 0
END DATE: Tue Jul 29 09:34:53 2008
[mukatira@sjmemmps02 NEXTGEN_SEQ]$ hawkeye chrM.bnk/
Opening chrM.bnk/... ERROR in openBank():
WHAT: Could not open bank file, chrM.bnk//CTG.ifo, No such file or directory
LINE: 1037
FILE: Bank_AMOS.cc
Segmentation fault
Hello,
Could you please post an example sequence and quality record from the .ace file? Hawkeye is complaining because either the consensus quality values are missing, or there is a mismatch between the number of bases in the consensus and the number of quality values.