search

dfguan / purge_dups

haplotypic duplication identification tool
MIT License
209 stars 21 forks source link

Error in `pbcstat' #137

Open YanCheer opened 10 months ago

YanCheer commented 10 months ago

Hi! Dengfeng. At the step 1, I used pbcstat to produce PB.base.cov and PB.stat files for my *.paf.gz with sizes of ~100 Mb (the pafs were generated as minimap2 -t 24 -x map-hifi $WordDir/$Pri_asm $InDir/$HiFi_reads |gzip -c > $OutDir/Pri_asm.paf.gz ). Howeve, it reported errors as follows:

[M::aa_pb] calculating coverage for each base on genome [M::aa_pb] print coverage histogram for the contigs Error in `pbcstat': free(): invalid size: 0x0000000000e39330 ======= Backtrace: ========= /lib64/libc.so.6(+0x81329)[0x7f221e2b0329] pbcstat[0x402754] pbcstat[0x4037be] pbcstat[0x403bc8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f221e251555] pbcstat[0x400d59] ======= Memory map: ======== 00400000-00407000 r-xp 00000000 08:00 2504884622 /projects/ yancheer/softwares/purge_dups/bin/pbcstat 00606000-00607000 r--p 00006000 08:00 2504884622 /projects/ yancheer/softwares/purge_dups/bin/pbcstat 00607000-00608000 rw-p 00007000 08:00 2504884622 /projects/ yancheer/softwares/purge_dups/bin/pbcstat 00dc1000-01ae9000 rw-p 00000000 00:00 0 [heap] 7f2214000000-7f2214021000 rw-p 00000000 00:00 0 7f2214021000-7f2218000000 ---p 00000000 00:00 0 7f2218b3f000-7f2218c00000 rw-p 00000000 00:00 0 7f2218c00000-7f2218cc1000 rw-p 00000000 00:00 0 7f2218cc1000-7f2218d22000 rw-p 00000000 00:00 0 7f2218d22000-7f2218d83000 rw-p 00000000 00:00 0 7f2218d83000-7f2218de4000 rw-p 00000000 00:00 0 7f2218de4000-7f2218e15000 rw-p 00000000 00:00 0 7f2218e15000-7f2218e76000 rw-p 00000000 00:00 0 7f2218e76000-7f2218ff7000 rw-p 00000000 00:00 0 7f2219026000-7f2219057000 rw-p 00000000 00:00 0 7f2219057000-7f22190b8000 rw-p 00000000 00:00 0 7f22190b8000-7f2219119000 rw-p 00000000 00:00 0 7f2219119000-7f22191da000 rw-p 00000000 00:00 0 7f22191da000-7f221929b000 rw-p 00000000 00:00 0 7f22192cb000-7f22192fc000 rw-p 00000000 00:00 0 7f22192fc000-7f221947d000 rw-p 00000000 00:00 0 7f22194ac000-7f22194dd000 rw-p 00000000 00:00 0 7f22194dd000-7f221953e000 rw-p 00000000 00:00 0 7f221953e000-7f22195ff000 rw-p 00000000 00:00 0 7f22195ff000-7f2219660000 rw-p 00000000 00:00 0 7f2219660000-7f2219721000 rw-p 00000000 00:00 0 7f2219721000-7f2219782000 rw-p 00000000 00:00 0 7f2219782000-7f2219903000 rw-p 00000000 00:00 0 7f2219903000-7f2219c04000 rw-p 00000000 00:00 0 7f2219c04000-7f2219d85000 rw-p 00000000 00:00 0 7f2219d85000-7f2219e46000 rw-p 00000000 00:00 0 7f2219e46000-7f2219f07000 rw-p 00000000 00:00 0 7f2219f07000-7f221a088000 rw-p 00000000 00:00 0 7f221a088000-7f221a209000 rw-p 00000000 00:00 0 7f221a209000-7f221a38a000 rw-p 00000000 00:00 0 7f221a3b8000-7f221a44b000 rw-p 00000000 00:00 0 7f221a44b000-7f221a5cc000 rw-p 00000000 00:00 0 7f221a5cc000-7f221a68d000 rw-p 00000000 00:00 0 7f221a68d000-7f221a80e000 rw-p 00000000 00:00 0 7f221a80e000-7f221a98f000 rw-p 00000000 00:00 0 7f221a98f000-7f221ab10000 rw-p 00000000 00:00 0 7f221ab10000-7f221ac91000 rw-p 00000000 00:00 0 7f221ac91000-7f221b292000 rw-p 00000000 00:00 0 7f221b292000-7f221b593000 rw-p 00000000 00:00 0 7f221b593000-7f221b714000 rw-p 00000000 00:00 0 7f221b714000-7f221ba15000 rw-p 00000000 00:00 0 7f221ba15000-7f221bd16000 rw-p 00000000 00:00 0 7f221bd41000-7f221bda2000 rw-p 00000000 00:00 0 7f221bda2000-7f221bdd3000 rw-p 00000000 00:00 0 7f221bdd3000-7f221be34000 rw-p 00000000 00:00 0 7f221be34000-7f221be96000 rw-p 00000000 00:00 0 7f221be96000-7f221bef7000 rw-p 00000000 00:00 0 7f221bef7000-7f221bf58000 rw-p 00000000 00:00 0 7f221bf58000-7f221c0d9000 rw-p 00000000 00:00 0 7f221c0d9000-7f221c19a000 rw-p 00000000 00:00 0 7f221c19a000-7f221c49b000 rw-p 00000000 00:00 0 7f221c49b000-7f221c79c000 rw-p 00000000 00:00 0 7f221c79c000-7f221ca9d000 rw-p 00000000 00:00 0 7f221ca9d000-7f221cc1e000 rw-p 00000000 00:00 0 7f221cc1e000-7f221ccdf000 rw-p 00000000 00:00 0 7f221ccdf000-7f221cd40000 rw-p 00000000 00:00 0 7f221dba5000-7f221dbd6000 rw-p 00000000 00:00 0 7f221e035000-7f221e066000 rw-p 00000000 00:00 0 7f221e22f000-7f221e3f3000 r-xp 00000000 fd:00 33634618 /usr/lib64/libc-2.17.so 7f221e3f3000-7f221e5f2000 ---p 001c4000 fd:00 33634618 /usr/lib64/libc-2.17.so 7f221e5f2000-7f221e5f6000 r--p 001c3000 fd:00 33634618 /usr/lib64/libc-2.17.so 7f221e5f6000-7f221e5f8000 rw-p 001c7000 fd:00 33634618 /usr/lib64/libc-2.17.so 7f221e5f8000-7f221e5fd000 rw-p 00000000 00:00 0 7f221e5fd000-7f221e6fe000 r-xp 00000000 fd:00 33634626 /usr/lib64/libm-2.17.so 7f221e6fe000-7f221e8fd000 ---p 00101000 fd:00 33634626 /usr/lib64/libm-2.17.so 7f221e8fd000-7f221e8fe000 r--p 00100000 fd:00 33634626 /usr/lib64/libm-2.17.so 7f221e8fe000-7f221e8ff000 rw-p 00101000 fd:00 33634626 /usr/lib64/libm-2.17.so 7f221e8ff000-7f221e921000 r-xp 00000000 fd:00 35568753 /usr/lib64/ld-2.17.so 7f221eacf000-7f221ead3000 r--p 00000000 08:00 2486599787 /projects/ yancheer/softwares/miniconda3/lib/libgcc_s.so.1 7f221ead3000-7f221eae5000 r-xp 00004000 08:00 2486599787 /projects/ yancheer/softwares/miniconda3/lib/libgcc_s.so.1 7f221eae5000-7f221eae8000 r--p 00016000 08:00 2486599787 /projects/ yancheer/softwares/miniconda3/lib/libgcc_s.so.1 7f221eae8000-7f221eae9000 r--p 00019000 08:00 2486599787 /projects/ yancheer/softwares/miniconda3/lib/libgcc_s.so.1 7f221eae9000-7f221eaea000 rw-p 0001a000 08:00 2486599787 /projects/ yancheer/softwares/miniconda3/lib/libgcc_s.so.1 7f221eaea000-7f221eaed000 rw-p 00000000 00:00 0 7f221eb02000-7f221eb03000 rw-p 00000000 00:00 0 7f221eb03000-7f221eb06000 r--p 00000000 08:00 2486797437 /projects/ yancheer/softwares/miniconda3/lib/libz.so.1.2.13 7f221eb06000-7f221eb15000 r-xp 00003000 08:00 2486797437 /projects/ yancheer/softwares/miniconda3/lib/libz.so.1.2.13 7f221eb15000-7f221eb1c000 r--p 00012000 08:00 2486797437 /projects/ yancheer/softwares/miniconda3/lib/libz.so.1.2.13 7f221eb1c000-7f221eb1d000 r--p 00018000 08:00 2486797437 /projects/ yancheer/softwares/miniconda3/lib/libz.so.1.2.13 7f221eb1d000-7f221eb1e000 rw-p 00019000 08:00 2486797437 /projects/ yancheer/softwares/miniconda3/lib/libz.so.1.2.13 7f221eb1e000-7f221eb20000 rw-p 00000000 00:00 0 7f221eb20000-7f221eb21000 r--p 00021000 fd:00 35568753 /usr/lib64/ld-2.17.so 7f221eb21000-7f221eb22000 rw-p 00022000 fd:00 35568753 /usr/lib64/ld-2.17.so 7f221eb22000-7f221eb23000 rw-p 00000000 00:00 0 7fff07536000-7fff07558000 rw-p 00000000 00:00 0 [stack] 7fff0758d000-7fff0758f000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

Is there something wrong in my *paf.gz files, in the source code of pbcstat, or in the my cluster settings???

Thanks~

YanCheer commented 10 months ago

Even if I re-installed purge_dups from the conda source, it repoted the same errors as well.