tests on test_data fail

[sandoro]

1. Installed bamsurgeon with no problems.
2. Ran programs in surgeon-master/tests -- all failed with error:

   Target and donor are aligned to incompatable reference genomes!

3. Text below shows for program "test_svn.sh"
   o command for "test_snv.sh"
   o output from "test_snv.sh" to STDOUT
   o directory listing of out put files
4. The other two test programs showed similar results.

What can I do to correct the installation?
Thanks
--sandy

Sanford M.Orlow Phd
National Institutes of Health
Bethesda MD
sandor@mail.nih.gov
#301-496-5362

$ (cd testbin;./test_snv.sh 10 1 /fdb/igenomes/Homo_sapiens/Ensembl
/GRCh37 /Sequence/BWAIndex/genome.fa)
^ created directory: addsnv_logs_testregion_mut.bam
| creating tmp bam: tmpbam0.973639139619.bam
| len(readlist): 58
| copy number in snp region: 22 34166720 34166721 = 3.0
| adjusted VAF: 0.333333333333
| picked: 19
| wrote: 58 mutated: 19
|
TOTAL OF 638 LINES
|
| DEBUG: len(bamlist) 10
| merging, cmd: ['samtools', 'merge', '-f', 'tmp.merging.0.tmp.0.605064592051.muts.bam', 'tmpbam0.973639139619.bam', 'tmpbam0.864850773523.bam', 'tmpbam0.577943620935.bam', 'tmpbam0.155017835179.bam', 'tmpbam0.993849196129.bam', 'tmpbam0.0611915676721.bam', 'tmpbam0.740942761619.bam', 'tmpbam0.795170425721.bam', 'tmpbam0.360219175697.bam', 'tmpbam0.627406859454.bam']
| merge finished, renaming: tmp.merging.0.tmp.0.605064592051.muts.bam --> tmp.0.605064592051.muts.bam
| done making mutations, merging mutations into ../test_data/testregion.bam --> ../test_data/testregion_mut.bam
| Target and donor are aligned to incompatable reference genomes!

v addsnv.py failed.

TEST OUTPUT FILES

TEST_SNV_1:
drw-r-xr-x 2 4096 Feb 4 12:16 addsnv_logs_testregion_mut.bam
-rw-r--r-- 1 39627 Feb 3 13:17 test_snv.log
-rw-r--r-- 1 33951 Feb 3 13:16 tmp.0.605064592051.muts.bam

TEST_SNV_1/addsnv_logs_testregion_mut.bam:
-rw-r--r-- 1 10346 Feb 3 13:15 testregion_mut.bam.22_33702084_33702085.log
-rw-r--r-- 1 8611 Feb 3 13:15 testregion_mut.bam.22_33714964_33714965.log
-rw-r--r-- 1 8612 Feb 3 13:15 testregion_mut.bam.22_33769483_33769484.log
-rw-r--r-- 1 7935 Feb 3 13:15 testregion_mut.bam.22_33908770_33908771.log
-rw-r--r-- 1 8616 Feb 3 13:15 testregion_mut.bam.22_33926586_33926587.log
-rw-r--r-- 1 8605 Feb 3 13:16 testregion_mut.bam.22_33943910_33943911.log
-rw-r--r-- 1 10156 Feb 3 13:15 testregion_mut.bam.22_33958087_33958088.log
-rw-r--r-- 1 8809 Feb 3 13:15 testregion_mut.bam.22_34141184_34141185.log
-rw-r--r-- 1 10011 Feb 3 13:14 testregion_mut.bam.22_34166720_34166721.log
-rw-r--r-- 1 9491 Feb 3 13:15 testregion_mut.bam.22_34264774_34264775.log

[adamewing]

Hi Sandy,

The issue is that the reference used for the tests must match the reference used for the alignment stored in BAM format. For the tests, this reference is compatible: http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta

You'll need to make a bwa reference (bwa index) and a samtools faidx reference.

Sorry for the confusion!

-Adam