Apply RepeatDetector to ONT data

[HLHsieh]

Hi there,

Thank you for providing this exciting tool. I am new to this field, so I hope my question is not too naive. After reviewing your paper, I understand that I can apply this algorithm to ONT, PacBio, and Illumina data. However, I did not notice any specific parameters mentioned for ONT data. I would appreciate it if you could offer me any suggestions or guidance on how to use RepeatDetector with ONT data.

Thank you for your help!

-- Hsin

[DionLab]

Hi Hsin,
Thanks for your interest. We have not successfully applied RD to ONT data as the data is too noisy (see Fig. S6). But we have not tired it yet on the newer chemistry/base calling.
Vincent

[HLHsieh]

Hi Vincent,

Thank you for your prompt response. Yes, you did mention this point in your article, but I missed it.

Additionally, I was trying to install RD, but I encountered some errors during the "make" step. Here are the error messages I received:

[  1%] Performing update step for 'gtest'
HEAD is now at ec44c6c1 Merge pull request #821 from mazong1123/master
[  2%] Performing patch step for 'gtest'
patching file googletest/scripts/pump.py
Reversed (or previously applied) patch detected!  Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file googletest/scripts/pump.py.rej
[  3%] No configure step for 'gtest'
[  4%] No build step for 'gtest'
[  5%] No install step for 'gtest'
[  6%] Completed 'gtest'
[  8%] Built target gtest
[  9%] Performing update step for 'htslib'
Fetching submodule htscodecs
Already up to date.
[ 10%] No patch step for 'htslib'
[ 11%] Performing configure step for 'htslib'
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether _XOPEN_SOURCE is declared... no
checking C compiler flags needed for ssse3... -mssse3
checking C compiler flags needed for popcnt... -mpopcnt
checking C compiler flags needed for sse4.1... -msse4.1
checking C compiler flags needed for avx2... -mavx2
checking C compiler flags needed for avx512f... -mavx512f
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking whether the linker supports versioned symbols... yes
checking whether the compiler accepts -fvisibility=hidden... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking whether htscodecs files are present... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
config.status: linking htscodecs_bundled.mk to htscodecs.mk
[ 12%] Performing build step for 'htslib'
[ 13%] No install step for 'htslib'
[ 14%] Completed 'htslib'
[ 16%] Built target htslib
[ 17%] Performing download step (download, verify and extract) for 'Boost'
-- File already exists but no hash specified (use URL_HASH):
  file='/hsinlun/bin/RepeatDetector/RepeatDetector/build/external/Boost/src/boost_1_65_1.tar.bz2'
Old file will be removed and new file downloaded from URL.
-- Downloading...
   dst='/hsinlun/bin/RepeatDetector/RepeatDetector/build/external/Boost/src/boost_1_65_1.tar.bz2'
   timeout='60 seconds'
   inactivity timeout='none'
-- Using src='https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2'
CMake Error at Boost-stamp/download-Boost.cmake:170 (message):
  Each download failed!

    error: downloading 'https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2' failed
          status_code: 22
          status_string: "HTTP response code said error"
          log:
          --- LOG BEGIN ---
            Trying 44.195.121.2...

  TCP_NODELAY set

  Connected to dl.bintray.com (44.195.121.2) port 443 (#0)

  ALPN, offering http/1.1

  successfully set certificate verify locations:

    CAfile: /etc/pki/tls/certs/ca-bundle.crt
    CApath: none

  [5 bytes data]

  TLSv1.3 (OUT), TLS handshake, Client hello (1):

  [512 bytes data]

  [5 bytes data]

  TLSv1.3 (IN), TLS handshake, Server hello (2):

  [112 bytes data]

  [5 bytes data]

  TLSv1.2 (IN), TLS handshake, Certificate (11):

  [4394 bytes data]

  [5 bytes data]

  TLSv1.2 (IN), TLS handshake, Server key exchange (12):

  [300 bytes data]

  [5 bytes data]

  TLSv1.2 (IN), TLS handshake, Server finished (14):

  [4 bytes data]

  [5 bytes data]

  TLSv1.2 (OUT), TLS handshake, Client key exchange (16):

  [37 bytes data]

  [5 bytes data]

  TLSv1.2 (OUT), TLS change cipher, Change cipher spec (1):

  [1 bytes data]

  [5 bytes data]

  TLSv1.2 (OUT), TLS handshake, Finished (20):

  [16 bytes data]

  [5 bytes data]

  [5 bytes data]

  TLSv1.2 (IN), TLS handshake, Finished (20):

  [16 bytes data]

  SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384

  ALPN, server accepted to use http/1.1

  Server certificate:

   subject: CN=*.bintray.com
   start date: Nov 14 00:00:00 2022 GMT
   expire date: Nov  9 23:59:59 2023 GMT
   subjectAltName: host "dl.bintray.com" matched cert's "*.bintray.com"
   issuer: C=US; O=DigiCert, Inc.; CN=GeoTrust Global TLS RSA4096 SHA256 2022 CA1
   SSL certificate verify ok.

  [5 bytes data]
  GET /boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2 HTTP/1.1
  Host: dl.bintray.com
  User-Agent: curl/7.61.1
  Accept: */*

  [5 bytes data]
  The requested URL returned error: 404 Not Found
  Closing connection 0
  [5 bytes data]
  TLSv1.2 (OUT), TLS alert, close notify (256):
  [2 bytes data]

          --- LOG END ---


make[2]: *** [libprf/CMakeFiles/Boost.dir/build.make:98: external/Boost/src/Boost-stamp/Boost-download] Error 1
make[1]: *** [CMakeFiles/Makefile2:1184: libprf/CMakeFiles/Boost.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

Based on my review of some related issues, I suspect this issue might be caused by the Boost library (as mentioned in this link: ethereum-mining/ethminer#2309). I was wondering if there is anything I can do in your code to resolve this problem.

Many thanks,
Hsin

[DionLab]

We are in between bioinformatician, so it will take a bit longer to get back to you on this. Sorry!