#1 -mapsnp fails to terminate

[Brian Walenz]

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ESTmapper/assembleOutput-- Not mRNA and not EST, so not picking the best polish.

/Users/m043472/estmapper/kmer/trunk/bin/terminate -P /Users/m043472/genomes/test/tmpmap/polishes-best /Users/m043472/genomes/test/tmpmap/cDNA-best.fasta -P /Users/m043472/genomes/test/tmpmap/polishes-good /Users/m043472/genomes/test/tmpmap/cDNA-good.fasta -I /Users/m043472/genomes/test/tmpmap/zero-hit-iid /Users/m043472/genomes/test/tmpmap/cDNA-zero.fasta -O /Users/m043472/genomes/test/tmpmap/cDNA-missing.fasta -i /Users/m043472/genomes/test/tmpmap/0-input/cDNA.fastaRUNNING------------------
/Users/m043472/estmapper/kmer/trunk/bin/terminate -P /Users/m043472/genomes/test/tmpmap/polishes-best /Users/m043472/genomes/test/tmpmap/cDNA-best.fasta -P /Users/m043472/genomes/test/tmpmap/polishes-good /Users/m043472/genomes/test/tmpmap/cDNA-good.fasta -I /Users/m043472/genomes/test/tmpmap/zero-hit-iid /Users/m043472/genomes/test/tmpmap/cDNA-zero.fasta -O /Users/m043472/genomes/test/tmpmap/cDNA-missing.fasta -i /Users/m043472/genomes/test/tmpmap/0-input/cDNA.fasta

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iidReaderWriter-- can't open '/Users/m043472/genomes/test/tmpmap/polishes-best': No such file or directory

ERROR: /Users/m043472/estmapper/kmer/trunk/bin/terminate -P /Users/m043472/genomes/test/tmpmap/polishes-best /Users/m043472/genomes/test/tmpmap/cDNA-best.fasta -P /Users/m043472/genomes/test/tmpmap/polishes-good /Users/m043472/genomes/test/tmpmap/cDNA-good.fasta -I /Users/m043472/genomes/test/tmpmap/zero-hit-iid /Users/m043472/genomes/test/tmpmap/cDNA-zero.fasta -O /Users/m043472/genomes/test/tmpmap/cDNA-missing.fasta -i /Users/m043472/genomes/test/tmpmap/0-input/cDNA.fasta
failed with exit status 1

Failed.

the directory of tmpmap:

R0163946:~/genomes/test m043472$ cd tmpmap
R0163946:~/genomes/test/tmpmap m043472$ ls
0-input/ 2-filter/ polishes-aborted zero-hit-iid
1-search/ 3-polish/ polishes-good
R0163946:~/genomes/test/tmpmap m043472$ ls -l
total 24
drwxr-xr-x 5 m043472 m043472 170 Mar 20 10:40 0-input/
drwxr-xr-x 60 m043472 m043472 2040 Mar 20 10:44 1-search/
drwxr-xr-x 5 m043472 m043472 170 Mar 20 10:44 2-filter/
drwxr-xr-x 10 m043472 m043472 340 Mar 20 10:44 3-polish/
-rw-r--r-- 1 m043472 m043472 0 Mar 20 10:44 polishes-aborted
-rw-r--r-- 1 m043472 m043472 12076 Mar 20 10:44 polishes-good
-rw-r--r-- 1 m043472 m043472 0 Mar 20 10:44 zero-hit-iid