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gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
MIT License
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*** stack smashing detected ***: gffread terminated #134

Open dengyang111 opened 7 months ago

dengyang111 commented 7 months ago

Hi, when i ran gffread, there was a bug. How should id resolve it. Thanks. Code and bug info: (m6A) [dengy@mu01 00_genome]$ gffread -T Ath_genomic.gff -o 1235 stack smashing detected : gffread terminated ======= Backtrace: ========= /usr/lib64/libc.so.6(__fortify_fail+0x37)[0x2ba7e179c6e7] /usr/lib64/libc.so.6(+0x1186a2)[0x2ba7e179c6a2] gffread(+0xf505)[0x562cba3be505] gffread(+0x3a59)[0x562cba3b2a59] /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ba7e16a6445] gffread(+0x47e9)[0x562cba3b37e9] ======= Memory map: ======== 2ba7e1460000-2ba7e1482000 r-xp 00000000 08:04 32118990 /usr/lib64/ld-2.17.so 2ba7e1482000-2ba7e1483000 rw-p 00000000 00:00 0 2ba7e1483000-2ba7e152c000 r--p 00000000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32 2ba7e152c000-2ba7e15cc000 r-xp 000a9000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32 2ba7e15cc000-2ba7e1653000 r--p 00149000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32 2ba7e1653000-2ba7e165e000 r--p 001cf000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32 2ba7e165e000-2ba7e1662000 rw-p 001da000 08:10 8602413582 /home/dengy/mambaforge/envs/m6A/lib/libstdc++.so.6.0.32 2ba7e1662000-2ba7e166f000 rw-p 00000000 00:00 0 2ba7e1681000-2ba7e1682000 r--p 00021000 08:04 32118990 /usr/lib64/ld-2.17.so 2ba7e1682000-2ba7e1683000 rw-p 00022000 08:04 32118990 /usr/lib64/ld-2.17.so 2ba7e1683000-2ba7e1684000 rw-p 00000000 00:00 0 2ba7e1684000-2ba7e1847000 r-xp 00000000 08:04 32118997 /usr/lib64/libc-2.17.so 2ba7e1847000-2ba7e1a46000 ---p 001c3000 08:04 32118997 /usr/lib64/libc-2.17.so 2ba7e1a46000-2ba7e1a4a000 r--p 001c2000 08:04 32118997 /usr/lib64/libc-2.17.so 2ba7e1a4a000-2ba7e1a4c000 rw-p 001c6000 08:04 32118997 /usr/lib64/libc-2.17.so 2ba7e1a4c000-2ba7e1a51000 rw-p 00000000 00:00 0 2ba7e1a51000-2ba7e1b52000 r-xp 00000000 08:04 32119005 /usr/lib64/libm-2.17.so 2ba7e1b52000-2ba7e1d51000 ---p 00101000 08:04 32119005 /usr/lib64/libm-2.17.so 2ba7e1d51000-2ba7e1d52000 r--p 00100000 08:04 32119005 /usr/lib64/libm-2.17.so 2ba7e1d52000-2ba7e1d53000 rw-p 00101000 08:04 32119005 /usr/lib64/libm-2.17.so 2ba7e1d53000-2ba7e1d5a000 r-xp 00000000 08:04 32119027 /usr/lib64/librt-2.17.so 2ba7e1d5a000-2ba7e1f59000 ---p 00007000 08:04 32119027 /usr/lib64/librt-2.17.so 2ba7e1f59000-2ba7e1f5a000 r--p 00006000 08:04 32119027 /usr/lib64/librt-2.17.so 2ba7e1f5a000-2ba7e1f5b000 rw-p 00007000 08:04 32119027 /usr/lib64/librt-2.17.so 2ba7e1f5b000-2ba7e1f5f000 r--p 00000000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1 2ba7e1f5f000-2ba7e1f71000 r-xp 00004000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1 2ba7e1f71000-2ba7e1f74000 r--p 00016000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1 2ba7e1f74000-2ba7e1f75000 r--p 00019000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1 2ba7e1f75000-2ba7e1f76000 rw-p 0001a000 08:10 19584214064 /home/dengy/mambaforge/envs/m6A/lib/libgcc_s.so.1 2ba7e1f76000-2ba7e1f8d000 r-xp 00000000 08:04 32119023 /usr/lib64/libpthread-2.17.so 2ba7e1f8d000-2ba7e218c000 ---p 00017000 08:04 32119023 /usr/lib64/libpthread-2.17.so 2ba7e218c000-2ba7e218d000 r--p 00016000 08:04 32119023 /usr/lib64/libpthread-2.17.so 2ba7e218d000-2ba7e218e000 rw-p 00017000 08:04 32119023 /usr/lib64/libpthread-2.17.so 2ba7e218e000-2ba7e2192000 rw-p 00000000 00:00 0 2ba7e293f000-2ba7e2ac0000 rw-p 00000000 00:00 0 562cba3af000-562cba3b1000 r--p 00000000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread 562cba3b1000-562cba3e1000 r-xp 00002000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread 562cba3e1000-562cba3ed000 r--p 00032000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread 562cba3ed000-562cba3ee000 r--p 0003e000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread 562cba3ee000-562cba3ef000 rw-p 0003f000 08:10 83855363104 /home/dengy/mambaforge/envs/m6A/bin/gffread 562cba3ef000-562cba3f7000 rw-p 00000000 00:00 0 562cbab9c000-562cc3a43000 rw-p 00000000 00:00 0 [heap] 7ffc9e687000-7ffc9e6aa000 rw-p 00000000 00:00 0 [stack] 7ffc9e796000-7ffc9e798000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted

gpertea commented 7 months ago

Can you point me to that Ath_genomic.gff file so I can check/debug this ? Also, I see this is a conda version of gffread, what does gffread --version show?

dengyang111 commented 7 months ago

Yes, this is a conda version and gffread --version showed is '0.12.7' [Uploading Ath_genomic.gff.tar.gz…]()

dengyang111 commented 7 months ago

[Uploading Ath_genomic.gff.tar.gz…]() [Uploading Ath_genomic.gff.tar.gz…]()

xiekunwhy commented 4 months ago

same problem happen.