<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">They are warnings from makeblastdb. It depends on what version of BLAST you have installed. Either upgrade or downgrade to get them to go away. They are just warnings and not errors though, so you can safely ignore them. They are just really annoying.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 23, 2017, at 10:47 AM, Daniel Ence <<a href="mailto:dandence@gmail.com" class="">dandence@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Chris, I haven’t seen that warning either in my usage of MAKER. My guess is that the version of Repeatmasker installed on your cluster has this warning and expects a certain format in the fasta headers. This could be checked by looking at the TE protein file that maker is using. Do you have access to that? <div class=""><br class=""></div><div class="">In any case it probably isn’t an issue that needs to be fixed if the output otherwise looks good. <br class=""><div class=""><br class=""></div><div class="">~Daniel<br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 23, 2017, at 12:26 PM, Willett, Christopher S <<a href="mailto:willett4@email.unc.edu" class="">willett4@email.unc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hello-
<div class=""><br class="">
</div>
<div class="">I have been using MAKER to annotate the genome of a copepod species on a cluster at my university and I had one question about a warning that keeps coming up (and I didn’t see this problem discussed in the archives of the google group). This warning
is happening even when I am running the test files so perhaps it is an issue with the installation on our server. It looks like it is a problem with the default TE protein file that maker is generating that spits out a bunch of warnings for each contig (see
below). It appears that the program is running fine otherwise and the output looks good. I was wondering if this is a problem that I have to address or if I can go ahead and just use the results and ignore this warning? I am using MAKER 2.31.8.</div>
<div class=""><br class="">
</div>
<div class="">Thanks for your help,</div>
<div class=""><br class="">
</div>
<div class="">Best, </div>
<div class=""><br class="">
</div>
<div class="">Chris Willett</div>
<div class=""><br class="">
</div>
<div class="">here is a portion of the run log with some examples of the warnings:</div>
<div class=""><br class="">
</div>
<div class="">------------------------------------------------------------<br class="">
# LSBATCH: User input<br class="">
maker<br class="">
------------------------------------------------------------<br class="">
<br class="">
Successfully completed.<br class="">
<br class="">
Resource usage summary:<br class="">
<br class="">
CPU time : 59.63 sec.<br class="">
Total Requested Memory : 0.50 GB<br class="">
Delta Memory : -<br class="">
Max Processes : 7<br class="">
Max Threads : 8<br class="">
Run time : 47 sec.<br class="">
Turnaround time : 55 sec.<br class="">
<br class="">
The output (if any) follows:<br class="">
<br class="">
STATUS: Parsing control files...<br class="">
STATUS: Processing and indexing input FASTA files...<br class="">
STATUS: Setting up database for any GFF3 input...<br class="">
A data structure will be created for you at:<br class="">
/proj/willetlb/users/cwillett/MAKER_analyses/data_test/dpp_contig.maker.output/dpp_contig_datastore<br class="">
<br class="">
To access files for individual sequences use the datastore index:<br class="">
/proj/willetlb/users/cwillett/MAKER_analyses/data_test/dpp_contig.maker.output/dpp_contig_master_datastore_index.log<br class="">
<br class="">
STATUS: Now running MAKER...<br class="">
examining contents of the fasta file and run log<br class="">
<br class="">
<br class="">
<br class="">
--Next Contig--<br class="">
<br class="">
#---------------------------------------------------------------------<br class="">
Now starting the contig!!<br class="">
SeqID: contig-dpp-500-500<br class="">
Length: 32156<br class="">
#---------------------------------------------------------------------<br class="">
<br class="">
<br class="">
setting up GFF3 output and fasta chunks<br class="">
doing repeat masking<br class="">
running repeat masker.<br class="">
#--------- command -------------#<br class="">
Widget::RepeatMasker:<br class="">
cd /tmp/maker_U9T1oG; /nas02/apps/repeatmasker-4.0.5/RepeatMasker/RepeatMasker /proj/willetlb/users/cwillett/MAKER_analyses/data_test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb
-species all -dir /proj/willetlb/users/cwillett/MAKER_analyses/data_test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1<br class="">
#-------------------------------#<br class="">
doing blastx repeats<br class="">
formating database...<br class="">
#--------- command -------------#<br class="">
Widget::formater:<br class="">
/nas02/apps/repeatmasker-4.0.5/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_U9T1oG/0/blastprep/te_proteins%2Efasta.mpi.10.0<br class="">
#-------------------------------#<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 3121 characters (max is 1000)<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1667 characters (max is 1000)<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1158 characters (max is 1000)<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 2237 characters (max is 1000)<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 1038 characters (max is 1000)<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
running blast search.<br class="">
#--------- command -------------#<br class="">
Widget::blastx:<br class="">
/nas02/apps/repeatmasker-4.0.5/rmblast-2.2.28/bin/blastx -db /tmp/maker_U9T1oG/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_U9T1oG/0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads
1 -seg yes -soft_masking true -lcase_masking -show_gis -out /proj/willetlb/users/cwillett/MAKER_analyses/data_test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner<br class="">
#-------------------------------#<br class="">
deleted:0 hits<br class="">
doing blastx repeats<br class="">
formating database...<br class="">
#--------- command -------------#<br class="">
Widget::formater:<br class="">
/nas02/apps/repeatmasker-4.0.5/rmblast-2.2.28/bin/makeblastdb -dbtype prot -in /tmp/maker_U9T1oG/0/blastprep/te_proteins%2Efasta.mpi.10.1<br class="">
#-------------------------------#<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.<br class="">
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Title is very long: 4311 characters (max is 1000)</div>
<div class=""><br class="">
</div>
<div class="">(continues on as above but title lengths are different)</div>
<br class="">
<div class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">
<div style="font-size: 12px; margin: 0px;" class="">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">Research Associate Professor</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">Department of Biology</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">CB#3280 Coker Hall</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">University of North Carolina, Chapel Hill</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">Chapel Hill, NC, 27599-3280 </font></div>
<div style="font-size: 12px; margin: 0px; min-height: 14px;" class=""><br class="">
</div>
<div style="font-size: 12px; margin: 0px; min-height: 14px;" class="">Office: <span style="text-align: -webkit-auto;" class="">2252 Genome Science Building</span></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">phone:<span class="Apple-tab-span" style="white-space: pre;">
</span>919-843-8663</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><font face="Helvetica" size="3" class="">fax:<span class="Apple-tab-span" style="white-space: pre;">
</span>919-962-1625</font></div>
<div style="font-size: 12px; margin: 0px;" class=""><br class="">
</div><p style="font-size: 12px; margin: 0px;" class=""></p>
<div style="font-size: 12px; margin: 0px;" class=""><a href="http://labs.bio.unc.edu/Willett/" class="">http://labs.bio.unc.edu/Willett/</a></div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br class=""></div></blockquote></div><br class=""></div></div></div></div>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>