theavanrossum
commented
1 year ago Hi Nik, sorry to hear you're encountering this error. Please see issues https://github.com/metasnv-tool/metaSNV/issues/2 and https://github.com/metasnv-tool/metaSNV/issues/3 for a possible fix.
Hi all,
I am trying to used metaSNV v2.0.4 to call genetic variants in a metagenomic dataset which was generated by sequencing of plant roots using a HiSeq. Prior to the SNV calling I to:
However, I encounter an error when I try to use the resulting bam file to call SNVs using metaSNV: standard out: (metasnv_nik) nkiel@dell-node-13:/netscratch/dep_psl/grp_rgo/kieln/tools$ $meta_path $dir runlist $ref --threads 4 Printing details in /netscratch/dep_psl/grp_rgo/kieln/tools/test/cov/out.bam.cov.detail! Probably really good coverage, since variables overrun! That's a big sum: 23346832... Error in `/netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute': munmap_chunk(): invalid pointer: 0x0000560d1ecabe60 ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x70bfb)[0x7f2bb6182bfb] /lib/x86_64-linux-gnu/libc.so.6(+0x76fc6)[0x7f2bb6188fc6] /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute(+0x282b)[0x560d1d77582b] /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute(+0x3b33)[0x560d1d776b33] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7f2bb61322e1] /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute(+0x1aca)[0x560d1d774aca] ======= Memory map: ======== 560d1d773000-560d1d77d000 r-xp 00000000 00:39 6942339799 /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute 560d1d97c000-560d1d97d000 r--p 00009000 00:39 6942339799 /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute 560d1d97d000-560d1d97e000 rw-p 0000a000 00:39 6942339799 /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute 560d1ec6f000-560d1ecc9000 rw-p 00000000 00:00 0 [heap] 7f2bb4e48000-7f2bb6112000 rw-p 00000000 00:00 0 7f2bb6112000-7f2bb62a7000 r-xp 00000000 08:03 24380101 /lib/x86_64-linux-gnu/libc-2.24.so 7f2bb62a7000-7f2bb64a7000 ---p 00195000 08:03 24380101 /lib/x86_64-linux-gnu/libc-2.24.so 7f2bb64a7000-7f2bb64ab000 r--p 00195000 08:03 24380101 /lib/x86_64-linux-gnu/libc-2.24.so 7f2bb64ab000-7f2bb64ad000 rw-p 00199000 08:03 24380101 /lib/x86_64-linux-gnu/libc-2.24.so 7f2bb64ad000-7f2bb64b1000 rw-p 00000000 00:00 0 7f2bb64b1000-7f2bb64c9000 r-xp 00000000 08:03 24380116 /lib/x86_64-linux-gnu/libpthread-2.24.so 7f2bb64c9000-7f2bb66c8000 ---p 00018000 08:03 24380116 /lib/x86_64-linux-gnu/libpthread-2.24.so 7f2bb66c8000-7f2bb66c9000 r--p 00017000 08:03 24380116 /lib/x86_64-linux-gnu/libpthread-2.24.so 7f2bb66c9000-7f2bb66ca000 rw-p 00018000 08:03 24380116 /lib/x86_64-linux-gnu/libpthread-2.24.so 7f2bb66ca000-7f2bb66ce000 rw-p 00000000 00:00 0 7f2bb66ce000-7f2bb67d1000 r-xp 00000000 08:03 24380105 /lib/x86_64-linux-gnu/libm-2.24.so 7f2bb67d1000-7f2bb69d0000 ---p 00103000 08:03 24380105 /lib/x86_64-linux-gnu/libm-2.24.so 7f2bb69d0000-7f2bb69d1000 r--p 00102000 08:03 24380105 /lib/x86_64-linux-gnu/libm-2.24.so 7f2bb69d1000-7f2bb69d2000 rw-p 00103000 08:03 24380105 /lib/x86_64-linux-gnu/libm-2.24.so 7f2bb69d2000-7f2bb6a61000 r-xp 00000000 00:40 402900 /home/nkiel/.conda/envs/metasnv_nik/lib/libhts.so.1.3 7f2bb6a61000-7f2bb6c60000 ---p 0008f000 00:40 402900 /home/nkiel/.conda/envs/metasnv_nik/lib/libhts.so.1.3 7f2bb6c60000-7f2bb6c62000 rw-p 0008e000 00:40 402900 /home/nkiel/.conda/envs/metasnv_nik/lib/libhts.so.1.3 7f2bb6c62000-7f2bb6c85000 r-xp 00000000 08:03 24379532 /lib/x86_64-linux-gnu/ld-2.24.so 7f2bb6c86000-7f2bb6c88000 rw-p 00000000 00:00 0 7f2bb6c88000-7f2bb6c8c000 r--p 00000000 00:40 353578 /home/nkiel/.conda/envs/metasnv_nik/lib/libgcc_s.so.1 7f2bb6c8c000-7f2bb6c9c000 r-xp 00004000 00:40 353578 /home/nkiel/.conda/envs/metasnv_nik/lib/libgcc_s.so.1 7f2bb6c9c000-7f2bb6c9f000 r--p 00014000 00:40 353578 /home/nkiel/.conda/envs/metasnv_nik/lib/libgcc_s.so.1 7f2bb6c9f000-7f2bb6ca0000 r--p 00016000 00:40 353578 /home/nkiel/.conda/envs/metasnv_nik/lib/libgcc_s.so.1 7f2bb6ca0000-7f2bb6ca1000 rw-p 00017000 00:40 353578 /home/nkiel/.conda/envs/metasnv_nik/lib/libgcc_s.so.1 7f2bb6cb3000-7f2bb6cb4000 rw-p 00000000 00:00 0 7f2bb6cb4000-7f2bb6d5a000 r--p 00000000 00:40 353183 /home/nkiel/.conda/envs/metasnv_nik/lib/libstdc++.so.6.0.30 7f2bb6d5a000-7f2bb6dee000 r-xp 000a6000 00:40 353183 /home/nkiel/.conda/envs/metasnv_nik/lib/libstdc++.so.6.0.30 7f2bb6dee000-7f2bb6e56000 r--p 0013a000 00:40 353183 /home/nkiel/.conda/envs/metasnv_nik/lib/libstdc++.so.6.0.30 7f2bb6e56000-7f2bb6e61000 r--p 001a1000 00:40 353183 /home/nkiel/.conda/envs/metasnv_nik/lib/libstdc++.so.6.0.30 7f2bb6e61000-7f2bb6e65000 rw-p 001ac000 00:40 353183 /home/nkiel/.conda/envs/metasnv_nik/lib/libstdc++.so.6.0.30 7f2bb6e65000-7f2bb6e68000 rw-p 00000000 00:00 0 7f2bb6e68000-7f2bb6e6b000 r--p 00000000 00:40 369186 /home/nkiel/.conda/envs/metasnv_nik/lib/libz.so.1.2.12 7f2bb6e6b000-7f2bb6e79000 r-xp 00003000 00:40 369186 /home/nkiel/.conda/envs/metasnv_nik/lib/libz.so.1.2.12 7f2bb6e79000-7f2bb6e80000 r--p 00011000 00:40 369186 /home/nkiel/.conda/envs/metasnv_nik/lib/libz.so.1.2.12 7f2bb6e80000-7f2bb6e81000 r--p 00017000 00:40 369186 /home/nkiel/.conda/envs/metasnv_nik/lib/libz.so.1.2.12 7f2bb6e81000-7f2bb6e82000 rw-p 00018000 00:40 369186 /home/nkiel/.conda/envs/metasnv_nik/lib/libz.so.1.2.12 7f2bb6e82000-7f2bb6e85000 rw-p 00000000 00:00 0 7f2bb6e85000-7f2bb6e86000 r--p 00023000 08:03 24379532 /lib/x86_64-linux-gnu/ld-2.24.so 7f2bb6e86000-7f2bb6e87000 rw-p 00024000 08:03 24379532 /lib/x86_64-linux-gnu/ld-2.24.so 7f2bb6e87000-7f2bb6e88000 rw-p 00000000 00:00 0 7fff6154f000-7fff61570000 rw-p 00000000 00:00 0 [stack] 7fff61588000-7fff6158b000 r--p 00000000 00:00 0 [vvar] 7fff6158b000-7fff6158d000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Failure in sample out.bamCall to /netscratch/dep_psl/grp_rgo/kieln/tools/metaSNV/src/qaTools/qaCompute -c 10 -d -i /netscratch/dep_psl/grp_rgo/kieln/tools/out.bam /netscratch/dep_psl/grp_rgo/kieln/tools/
Many thanks in advance!