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NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
https://www.nature.com/articles/s41598-018-23978-z
MIT License
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Error in the detection of indels step #22

Open James-Wong87 opened 2 years ago

James-Wong87 commented 2 years ago

Hi, recently I have been trying to run IMSindel on human whole-genome sequencing short-reads but have been running into an error and the program terminates without any output. When I checked the log file I see something like the following:

---------------------------------------------- LOG_FILE ------------------------------------------------------

Parameters: Avg. base quality: 20 Maping quality: 20 Read group: within 3bp paired B and F: within 5bp Support reads for making consensus sequence: 3 mimimum clipping fragment base: 5bp support clip length: 5bp bam: /home/james/GM18943_illumina_20211206/chrY/GM18943_aligned.sorted.remDup.chrY.bam chr: chrY outd: /home/kikemoto/IMSindel_NA18943/chrY/ indelsize: 10000 reffa: /home/james/GM18943_illumina_20211206/resource_files/resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta glsearch: /home/james/tools/fasta36-36.3.8/bin/glsearch36 glsearch mat: /home/james/tools/IMSindel-master/data/mydna.mat mafft: /home/james/tools/mafft-7.490-with-extensions/core/mafft samtools: /home/james/tools/samtools-1.14/samtools temp: /home/james/IMSindel_NA18943/tmp_imsindel/ thread: 1 exclude-region:

mafft version:

samtools version: samtools 1.14 Using htslib 1.14 Copyright (C) 2021 Genome Research Ltd.

Samtools compilation details: Features: build=configure curses=yes CC: /usr/local/package/gcc/7.3.0/bin/gcc CPPFLAGS: -I/usr/local/include CFLAGS: -Wall -I/usr/local/include LDFLAGS: -L/usr/local/lib64 -L/usr/local/lib HTSDIR: htslib-1.14 LIBS:
CURSES_LIB: -lncursesw

HTSlib compilation details: Features: build=configure plugins=no libcurl=yes S3=yes GCS=yes libdeflate=no lzma=yes bzip2=yes htscodecs=1.1.1-1-ged325d7 CC: /usr/local/package/gcc/7.3.0/bin/gcc CPPFLAGS: -I/usr/local/include CFLAGS: -Wall -I/usr/local/include -fvisibility=hidden LDFLAGS: -L/usr/local/lib64 -L/usr/local/lib -fvisibility=hidden

HTSlib URL scheme handlers present: built-in: preload, data, file S3 Multipart Upload: s3w, s3w+https, s3w+http Amazon S3: s3+https, s3+http, s3 Google Cloud Storage: gs+http, gs+https, gs libcurl: imaps, pop3, http, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, ldap, https, ldaps, tftp, pop3s, dict crypt4gh-needed: crypt4gh mem: mem

glsearch version: USAGE glsearch36 [-options] query_file library_file glsearch36 -help for a complete option list

DESCRIPTION GLSEARCH performs a global-query/local-library search version: 36.3.8i Sept, 2021 COMMON OPTIONS (options must preceed query_file library_file) -s: [BL50] scoring matrix; -f: [-12] gap-open penalty; -g: [-2] gap-extension penalty; -S filter lowercase (seg) residues; -b: high scores reported (limited by -E by default); -d: number of alignments shown (limited by -E by default); -I interactive mode;

  1. collecting indel related reads... /home/james/tools/samtools-1.14/samtools view -F 1024 -f 2 /home/james/GM18943_illumina_20211206/chrY/GM18943_aligned.sorted.remDup.chrY.bam chrY

    backward_clips: 20038

    forward_clips: 19978

    non_clips: 39022

  2. collecting indel related reads...done
  3. collecting unmapped reads... /home/james/tools/samtools-1.14/samtools view -F 1024 -f 8 /home/james/GM18943_illumina_20211206/chrY/GM18943_aligned.sorted.remDup.chrY.bam chrY mate_unmapped_read_names: 3771 /home/james/tools/samtools-1.14/samtools view -F 1024 -f 4 /home/james/GM18943_illumina_20211206/chrY/GM18943_aligned.sorted.remDup.chrY.bam chrY Insert size Avg: 463.15720669817136 SD: 167.52653227557147

    unmapped reads: 10537

  4. collecting unmapped reads...done
  5. considering support reads...

    backward clip with support reads: 624

    forward clip with support reads: 588

    non_clips with suport reads: 2554

  6. considering support reads...done
  7. making consensus seqs from support reads...

    backward clip with consensus: 624 --> 192

    forward clip with consensus: 588 --> 210

    shot indel with consensus: 2554 --> 1207

  8. making consensus seqs from support reads...done
  9. making consensus seq from B and F.. making consensus seq for long deletion...done
  10. detection of indels...

    paired long indel candidates: 29

    unpaired long indel candidates: 199

    short indel candidates: 1207

    error ---------------------------------------------- END_LOG_FILE ------------------------------------------------------

When I checked the error file that was created, the following error message was found:

------------------------------------------ ERROR_FILE: ------------------------------------------------------------------ v7.490 (2021/Oct/30) Error in `/home/james/tools/fasta36-36.3.8/bin/glsearch36': double free or corruption (out): 0x00000000006a4ab0 ======= Backtrace: ========= /lib64/libc.so.6(+0x81299)[0x2b7eaee8b299] /home/james/tools/fasta36-36.3.8/bin/glsearch36[0x41a1b6] /home/james/tools/fasta36-36.3.8/bin/glsearch36[0x4043d6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b7eaee2c555] /home/james/tools/fasta36-36.3.8/bin/glsearch36[0x4020b9] ======= Memory map: ======== 00400000-0044c000 r-xp 00000000 a11:1988 1567264058145577220 /yshare2/ZETTAI_path_WA_slash_home_KARA/home/james/tools/fasta36-36.3.8/bin/glsearch36 0064b000-0064c000 r--p 0004b000 a11:1988 1567264058145577220 /yshare2/ZETTAI_path_WA_slash_home_KARA/home/james/tools/fasta36-36.3.8/bin/glsearch36 0064c000-00659000 rw-p 0004c000 a11:1988 1567264058145577220 /yshare2/ZETTAI_path_WA_slash_home_KARA/home/james/tools/fasta36-36.3.8/bin/glsearch36 00659000-0065a000 rw-p 00000000 00:00 0 006a4000-006c5000 rw-p 00000000 00:00 0 [heap] 2b7eae6c8000-2b7eae6ea000 r-xp 00000000 08:03 40621 /usr/lib64/ld-2.17.so 2b7eae6ea000-2b7eae714000 rw-p 00000000 00:00 0 2b7eae724000-2b7eae74d000 rw-p 00000000 00:00 0 2b7eae8e9000-2b7eae8ea000 r--p 00021000 08:03 40621 /usr/lib64/ld-2.17.so 2b7eae8ea000-2b7eae8eb000 rw-p 00022000 08:03 40621 /usr/lib64/ld-2.17.so 2b7eae8eb000-2b7eae8ec000 rw-p 00000000 00:00 0 2b7eae8ec000-2b7eae9ed000 r-xp 00000000 08:03 40633 /usr/lib64/libm-2.17.so 2b7eae9ed000-2b7eaebec000 ---p 00101000 08:03 40633 /usr/lib64/libm-2.17.so 2b7eaebec000-2b7eaebed000 r--p 00100000 08:03 40633 /usr/lib64/libm-2.17.so 2b7eaebed000-2b7eaebee000 rw-p 00101000 08:03 40633 /usr/lib64/libm-2.17.so 2b7eaebee000-2b7eaec05000 r-xp 00000000 08:03 144325 /usr/lib64/libpthread-2.17.so 2b7eaec05000-2b7eaee04000 ---p 00017000 08:03 144325 /usr/lib64/libpthread-2.17.so 2b7eaee04000-2b7eaee05000 r--p 00016000 08:03 144325 /usr/lib64/libpthread-2.17.so 2b7eaee05000-2b7eaee06000 rw-p 00017000 08:03 144325 /usr/lib64/libpthread-2.17.so 2b7eaee06000-2b7eaee0a000 rw-p 00000000 00:00 0 2b7eaee0a000-2b7eaefcd000 r-xp 00000000 08:03 17625 /usr/lib64/libc-2.17.so 2b7eaefcd000-2b7eaf1cd000 ---p 001c3000 08:03 17625 /usr/lib64/libc-2.17.so 2b7eaf1cd000-2b7eaf1d1000 r--p 001c3000 08:03 17625 /usr/lib64/libc-2.17.so 2b7eaf1d1000-2b7eaf1d3000 rw-p 001c7000 08:03 17625 /usr/lib64/libc-2.17.so 2b7eaf1d3000-2b7eaf1d8000 rw-p 00000000 00:00 0 2b7eaf1d8000-2b7eaf1ee000 r-xp 00000000 08:03 823889101 /usr/local/package/gcc/7.3.0/lib64/libgcc_s.so.1 2b7eaf1ee000-2b7eaf3ed000 ---p 00016000 08:03 823889101 /usr/local/package/gcc/7.3.0/lib64/libgcc_s.so.1 2b7eaf3ed000-2b7eaf3ee000 r--p 00015000 08:03 823889101 /usr/local/package/gcc/7.3.0/lib64/libgcc_s.so.1 2b7eaf3ee000-2b7eaf3ef000 rw-p 00016000 08:03 823889101 /usr/local/package/gcc/7.3.0/lib64/libgcc_s.so.1 2b7eb0000000-2b7eb0021000 rw-p 00000000 00:00 0 2b7eb0021000-2b7eb4000000 ---p 00000000 00:00 0 7ffdba2be000-7ffdba2e0000 rw-p 00000000 00:00 0 [stack] 7ffdba3db000-7ffdba3dd000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

command exec error: pid 41193 SIGABRT (signal 6) (core dumped) check result and inputs of the following command /home/james/tools/fasta36-36.3.8/bin/glsearch36 -s /home/james/tools/IMSindel-master/data/mydna.mat -g0 -f20 /home/james/IMSindel_NA18943/tmp_imsindel/gls_seq20211217-28878-kp0lau /home/james/IMSindel_NA18943/tmp_imsindel/gls_ref20211217-28878-xyb773 ------------------------------------------------- END_ERROR_FILE ----------------------------------------------------------

I have downloaded and installed the newest versions of glsearch and mafft but that does not seem to solve the issue. Would appreciate if you could provide some insights into how the issue can be solved please? Thank you very much.

holrock commented 2 years ago

It looks like fasta's memory error. If input files are correct (/home/james/IMSindel_NA18943/tmp_imsindel/gls_seq20211217-28878-kp0lau /home/james/IMSindel_NA18943/tmp_imsindel/gls_ref20211217-28878-xyb773) you probably need to debug the fasta program or ask the developer.