Weird mafToFastaStitcher running error #39
Description
Hello
I am running mafToFastaStitcher command with test data: /data/01/p1/user157/software/mafTools/bin/mafToFastaStitcher -m input.maf --seqs input.fa --breakpointPenalty 5 --outMfa output.mfa
The input.maf is:
## maf version=1
a score=0.0 `status=test.input`
s ref.chr1 10 10 + 100 ACGTACGTAC
s seq1.chr@ 0 10 + 100 AAAAAAAAAA
s seq2.chr& 10 5 + 100 -----CCCCC
s seq6.chr1 10 5 + 100 -----GGGGG
s seq7.chr20 0 5 + 100 AAAAA-----
a score=0.0 status=test.input
s ref.chr1 20 10 + 100 GTACGTACGT
s seq2.chr!! 5 5 + 100 CCCCC-----
s seq3.chr0 20 5 + 100 -----GGGGG
s seq6.chr1 22 5 + 100 GGGGG-----
a score=0.0 status=test.input
s ref.chr1 30 10 + 100 ACGTACGTAC
s seq4.chr1 0 5 - 100 GG-----GGG
s seq5.chr2 0 10 + 100 CCCCCCCCCC
The input.fa is :
> ref.chr1
ggggggggggACGTACGTACGTACGTACGTACGTACGTACgg
> seq1.chr@
AAAAAAAAAAgg
> seq2.chr&
aaaaaaaaaaCCCCCaa
> seq2.chr!!
aaaaaCCCCCaa
> seq3.chr0
aaaaaaaaaaaaaaaaaaaGGGGGaa
seq4.chr1
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaCCCCC
> seq6.chr1
aaaaaaaaaGGGGGaaaaaaaGGGGGaa
> seq7.chr20
AAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAATT
However, I got the error:
[1] 3382482 abort (core dumped) /data/01/p1/user157/software/mafTools/bin/mafToFastaStitcher -m input.maf
The compilation for mafToFastaStitcher is correct with make test:
gcc -std=c99 -Wno-unused-but-set-variable -c src/mafToFastaStitcherAPI.c -o test/mafToFastaStitcherAPI.o.tmp -O3 -Wall -Werror --pedantic -funro$
l-loops -DNDEBUG -Wshadow -Wpointer-arith -Wstrict-prototypes -Wmissing-prototypes -I ../../sonLib/lib -I ../inc -I ../external -lm
mv test/mafToFastaStitcherAPI.o.tmp test/mafToFastaStitcherAPI.o
mkdir -p test/
gcc -std=c99 -Wno-unused-but-set-variable -c src/buildVersion.c -o test/buildVersion.o.tmp -O0 -g -Wall -Werror --pedantic -I ../../sonLib/lib -$
../inc -I ../external
mv test/buildVersion.o.tmp test/buildVersion.o
mkdir -p test/
gcc -std=c99 -Wno-unused-but-set-variable -c src/test.mafToFastaStitcherAPI.c -o test/test.mafToFastaStitcherAPI.o.tmp -O0 -g -Wall -Werror --pe$
antic -I ../../sonLib/lib -I ../inc -I ../external
mv test/test.mafToFastaStitcherAPI.o.tmp test/test.mafToFastaStitcherAPI.o
mkdir -p test/
gcc -std=c99 -Wno-unused-but-set-variable src/allTests.c test/sharedMaf.o test/common.o ../external/CuTest.a test/mafToFastaStitcherAPI.o ../../$
onLib/lib/sonLib.a test/buildVersion.o test/test.mafToFastaStitcherAPI.o -o test/allTests.tmp -O0 -g -Wall -Werror --pedantic -I ../../sonLib/li$
-I ../inc -I ../external -lm
mv test/allTests.tmp test/allTests
mkdir -p test/
gcc -std=c99 -Wno-unused-but-set-variable src/mafToFastaStitcher.c test/sharedMaf.o test/common.o ../external/CuTest.a test/mafToFastaStitcherAPI
.o ../../sonLib/lib/sonLib.a test/buildVersion.o -o test/mafToFastaStitcher.tmp -O0 -g -Wall -Werror --pedantic -I ../../sonLib/lib -I ../inc -I
../external -lm
mv test/mafToFastaStitcher.tmp test/mafToFastaStitcher
./test/allTests && python2.7 src/test.mafToFastaStitcher.py --verbose && rm -rf ./test/ && rmdir ./tempTestDir
Running test case test_readingFasta_0
Running test case test_newBlockHashFromBlock_0
Running test case test_addMafLineToRow_0
Running test case test_addMafLineToRow_1
Running test case test_penalize_0
Running test case test_interstitial_0
Running test case test_addBlockToHash_0
Running test case test_addBlockToHash_1
Running test case test_addBlockToHash_2
Running test case test_addBlockToHash_3
Running test case test_addBlockToHash_4
Running test case test_addBlockToHash_5
Running test case test_addBlockToHash_6
.............
OK (13 tests)
testAllTests (__main__.CuTest)
If valgrind is installed on the system, check for memory related errors in CuTests ... ok
testFastaStitch (__main__.FastaStitchTest)
mafToFastaStitcher should produce known output for a given known input ... ok
testMemory1 (__main__.FastaStitchTest)
If valgrind is installed on the system, check for memory related errors (1). ... ok
----------------------------------------------------------------------
Ran 3 tests in 19.287s
OK
And only running mafToFastaStitcher -h is normal:
mafToFastaStitcher, v0.1 Oct 2012
build: 2024-06-23T15:46CST, master, 4e5b5de3f275f61b36b9762824cc1edbead31820
Usage: mafToFastaStitcher --maf mafFile.maf --seqs seq1.fa,seq2.fa[,...] --breakpointPenalty 5 --interstitialSequence 20 --outMfa output.mfa
Options:
-h, --help show this message and exit.
-m, --maf path to the maf file.
--seqs comma separated list of fasta sequences. each fasta may contain
multiple entries. all sequences in the input alignment must be accounted
for with an element in a fasta.
--outMfa multiple sequence fasta output file.
--breakpointPenalty number of `N' characters to insert into a sequence
when a breakpoint is detected.
--interstitialSequence maximum length of interstitial sequence to be
added (from a fasta) into the fasta before a breakpoint is declared and
the <code>--breakpointPenalty</code> number of <code>N</code>'s is added
instead.
--outMaf multiple alignment format output file.
--reference optional. The name of the reference sequence. All intervening
reference sequence between the first and last block of the input --maf
will be read out in the output.
-v, --verbose turns on verbose output.
Could you give me any suggestions? Looking forward with your reply.
Best wishes
Na Wan