Missing Unit Test Data File?

[JWong42]

Hi,

I am trying to install the latest version of ALE but it is failing at the ./ALE --SNPreport part of the tests. When I check the PhiX.sam-testSNPPhiX.ale.log file, it says Error! Could not open assembly file: ../test/PhiX174-SNP.fsa. I think the PhiX174-SNP.fsa file might not yet be included in the test folder? Please see below for the logs. Thanks!

make -C samtools-0.1.19 lib make[1]: Entering directory /opt/ALE/src/samtools-0.1.19' make[1]: Nothing to be done forlib'. make[1]: Leaving directory `/opt/ALE/src/samtools-0.1.19' gcc -c -g -O3 -D_GNU_SRC samtools_helper.c -Isamtools-0.1.19 true gcc -g -O3 -D_GNU_SRC ALE.c ALElike.o ALEhelpers.o ssw.o -o ALE -lz -lm -Isamtools-0.1.19 -Lsamtools-0.1.19 -lbam samtoolshelper.o -lpthread ALE.c: In function ‘main’: ALE.c:137:15: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘char ’ [-Wformat] ALE.c:150:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘char ’ [-Wformat] rm -f ../test/_-testPhiX.ale\ ../test/-tinytestPhiX.ale ../test/-tinytestPhiX-broken.ale ../test/-testRealignPhiX.ale ../test/-testSNPPhiX.ale ./ALE ../test/PhiX-sort.bam ../test/PhiX174.fsa ../test/PhiX-sort.bam-testPhiX.ale > ../test/PhiX-sort.bam-testPhiX.ale.log 2>&1 && ls -l ../test/PhiX-sort.bam-testPhiX.ale -rw-r--r-- 1 jwong iplant-everyone 218332 Sep 27 17:03 ../test/PhiX-sort.bam-testPhiX.ale diff -q ../test/PhiX-sort.bam-testPhiX.ale ../test/PhiX-sort.ale > ../test/PhiX-sort.bam-testPhiX.ale.diff && echo "test1 PASSED" test1 PASSED ./ALE ../test/PhiX.bam ../test/PhiX174.fsa ../test/PhiX.bam-testPhiX.ale > ../test/PhiX.bam-testPhiX.ale.log 2>&1 && ls -l ../test/PhiX.bam-testPhiX.ale -rw-r--r-- 1 jwong iplant-everyone 218332 Sep 27 17:03 ../test/PhiX.bam-testPhiX.ale diff -q ../test/PhiX.bam-testPhiX.ale ../test/PhiX.ale > ../test/PhiX.bam-testPhiX.ale.diff && echo "test2 PASSED" test2 PASSED ./ALE ../test/PhiX.sam ../test/PhiX174.fsa ../test/PhiX.sam-testPhiX.ale > ../test/PhiX.sam-testPhiX.ale.log 2>&1 && ls -l ../test/PhiX.sam-testPhiX.ale -rw-r--r-- 1 jwong iplant-everyone 218332 Sep 27 17:03 ../test/PhiX.sam-testPhiX.ale diff -q ../test/PhiX.sam-testPhiX.ale ../test/PhiX.ale > ../test/PhiX.sam-testPhiX.ale.diff && echo "test3 PASSED" test3 PASSED ./ALE ../test/PhiX-tiny.sam ../test/PhiX174.fsa ../test/PhiX-tiny.sam-testPhiX.ale > ../test/PhiX-tiny.sam-testPhiX.ale.log 2>&1 && ls -l ../test/PhiX-tiny.sam-testPhiX.ale -rw-r--r-- 1 jwong iplant-everyone 235838 Sep 27 17:03 ../test/PhiX-tiny.sam-testPhiX.ale diff -q ../test/PhiX-tiny.sam-testPhiX.ale ../test/PhiX-tiny.ale > ../test/PhiX-tiny.sam-testPhiX.ale.diff && echo "test4 PASSED" test4 PASSED ./ALE --realign ../test/PhiX.sam ../test/PhiX174.fsa ../test/PhiX.sam-testRealignPhiX.ale > ../test/PhiX.sam-testRealignPhiX.ale.log 2>&1 && ls -l ../test/PhiX.sam-testRealignPhiX.ale -rw-r--r-- 1 jwong iplant-everyone 218332 Sep 27 17:03 ../test/PhiX.sam-testRealignPhiX.ale diff -q ../test/PhiX.sam-testRealignPhiX.ale ../test/PhiX.ale > ../test/PhiX.sam-testRealignPhiX.ale.diff && echo "test5 PASSED" test5 PASSED ./ALE --SNPreport ../test/PhiX.sam-testSNPPhiX.ale.SNPreport.txt ../test/PhiX.sam ../test/PhiX174-SNP.fsa ../test/PhiX.sam-testSNPPhiX.ale > ../test/PhiX.sam-testSNPPhiX.ale.log 2>&1 && ls -l ../test/PhiX.sam-testSNPPhiX.ale make: *\ [../test/PhiX.sam-testSNPPhiX.ale] Error 1

[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [samopen] SAM header is present: 1 sequences. Reporting SNP phasing into ../test/PhiX.sam-testSNPPhiX.ale.SNPreport.txt BAM file: ../test/PhiX.sam Assembly fasta file: ../test/PhiX174-SNP.fsa ALE Output file: ../test/PhiX.sam-testSNPPhiX.ale Checking if ../test/PhiX.sam is a SAM formatted file, instead of BAM Reading in assembly... Error! Could not open assembly file: ../test/PhiX174-SNP.fsa

[mkuhring]

I would really like to test ALE but I'm having the same problem. I'm wondering how other users get along without this file. Should the file actually be there from the start or is it created in the meantime? Or is the problem something else? For the sake of completeness, I'm using gcc 4.3.4 and make 3.81. Does ALE require something else to compile?

Thank you very much for your help. Best regards, mkuhring

[JWong42]

I just modified the makefile in src directory so that test6 doesn't get included in the test suite. The line I changed can be seen below. After that, you can compile it.

test: ALE cleantest test1 test2 test3 test4 test5 test-single-relations test-pair-relations test-pair-chimer-baseline test-pair-chimer

[mkuhring]

That's a good workaround, thanks.

[sc932]

Thanks for the fix. Applied the diff (test6 has been removed).

$make test now passes.