Music Smashing The Stack

Question

[fcaramia.work]

Hi guys,

I got the following error while running MuSIC..

Doesn’t look like an easy one to trace...

*** stack smashing detected ***: calcRoiCovg terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f9578108907]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x7f95781088d0]
calcRoiCovg[0x402c04]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f957801f76d]
calcRoiCovg[0x402059]
======= Memory map: ========
00400000-0041a000 r-xp 00000000 fc:01 158572                             /usr/bin/calcRoiCovg
00619000-0061a000 r--p 00019000 fc:01 158572                             /usr/bin/calcRoiCovg
0061a000-0061b000 rw-p 0001a000 fc:01 158572                             /usr/bin/calcRoiCovg
023bd000-023de000 rw-p 00000000 00:00 0                                  [heap]
7f9577de8000-7f9577dfd000 r-xp 00000000 fc:01 786479                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9577dfd000-7f9577ffc000 ---p 00015000 fc:01 786479                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9577ffc000-7f9577ffd000 r--p 00014000 fc:01 786479                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9577ffd000-7f9577ffe000 rw-p 00015000 fc:01 786479                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9577ffe000-7f95781b3000 r-xp 00000000 fc:01 797975                     /lib/x86_64-linux-gnu/libc-2.15.so
7f95781b3000-7f95783b2000 ---p 001b5000 fc:01 797975                     /lib/x86_64-linux-gnu/libc-2.15.so
7f95783b2000-7f95783b6000 r--p 001b4000 fc:01 797975                     /lib/x86_64-linux-gnu/libc-2.15.so
7f95783b6000-7f95783b8000 rw-p 001b8000 fc:01 797975                     /lib/x86_64-linux-gnu/libc-2.15.so
7f95783b8000-7f95783bd000 rw-p 00000000 00:00 0 
7f95783bd000-7f95783d3000 r-xp 00000000 fc:01 786662                     /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f95783d3000-7f95785d2000 ---p 00016000 fc:01 786662                     /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f95785d2000-7f95785d3000 r--p 00015000 fc:01 786662                     /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f95785d3000-7f95785d4000 rw-p 00016000 fc:01 786662                     /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f95785d4000-7f95786cd000 r-xp 00000000 fc:01 797984                     /lib/x86_64-linux-gnu/libm-2.15.so
7f95786cd000-7f95788cc000 ---p 000f9000 fc:01 797984                     /lib/x86_64-linux-gnu/libm-2.15.so
7f95788cc000-7f95788cd000 r--p 000f8000 fc:01 797984                     /lib/x86_64-linux-gnu/libm-2.15.so
7f95788cd000-7f95788ce000 rw-p 000f9000 fc:01 797984                     /lib/x86_64-linux-gnu/libm-2.15.so
7f95788ce000-7f95788f0000 r-xp 00000000 fc:01 797991                     /lib/x86_64-linux-gnu/ld-2.15.so
7f9578ae3000-7f9578ae6000 rw-p 00000000 00:00 0 
7f9578aed000-7f9578af0000 rw-p 00000000 00:00 0 
7f9578af0000-7f9578af1000 r--p 00022000 fc:01 797991                     /lib/x86_64-linux-gnu/ld-2.15.so
7f9578af1000-7f9578af3000 rw-p 00023000 fc:01 797991                     /lib/x86_64-linux-gnu/ld-2.15.so
7fff8bddc000-7fff8bdfd000 rw-p 00000000 00:00 0                          [stack]
7fff8bdff000-7fff8be00000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Failed to execute: calcRoiCovg /galaxy/database/files/010/dataset_10463.dat /galaxy/database/files/010/dataset_10464.dat     roi_jason /galaxy/indexes/human/g1k_v37/fasta/human_g1k_v37.fasta ./MuSIC_OUTPUT/roi_covgs/IC080.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "IC080        /galaxy/database/files/010/dataset_10463.dat    /galaxy/database/files/010/dataset_10464.dat" --roi-file "roi_jason" --reference-    sequence "/galaxy/indexes/human/g1k_v37/fasta/human_g1k_v37.fasta" --output-file "./MuSIC_OUTPUT/roi_covgs/IC080.covg"'

Answer 1

[Chris Miller]

In my experience, crashes in calcRoiCovg are generally due to mismatches between the bam file you provide and the reference fasta file. This often happens when the script tries to look off the end of a chromosome, due to differences in the reference.

Answer 2

[Cyriac Kandoth]

Agree with Chris. Also check your roi-file to make sure it uses 1-based start and stop loci... And that all the ROIs lie within chromosome bounds of reference fasta and the BAM files.

Answer 3

[fcaramia.work]

thank you for the feedback