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View Code? Open in Web Editor NEWFlip-flop basecaller for Oxford Nanopore reads
License: Other
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ihh jts jordisr diamanto alexpersa7 ttbond pythseq zovoilis-lab kedartatwawadi dohun-yi scdealy mamaship wook2013 tmassingham-portalflappie's Issues
Direct RNA
Would runnie work on direct RNA raw reads?
failed to initialize runtime: engine "" is not found
Hi-
When trying to run flappie in parallel I get the following error:
export OPENBLAS_NUM_THREADS=1
module load openblas/0.3.4
module load openmpi/4.0.1
find $reads_dir -name *fast5 | parallel -P 2 -X flappie --model r941_5mC > $output_file```
Thanks!
Linking C executable flappie errors
Hi,
I appear to be having the following error when trying to install flappie. Any assistance would be great.
Many thanks.
Damien
dct7@login04:~/flappie$ openblasRoot=/home/dct7/bin/ make flappie
cd build && \
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DHDF5_ROOT='' \
-DOPENBLAS_REDHAT='' \
-DOPENBLAS_ROOT=/home/dct7/bin/ && \
make flappie
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dct7/flappie/build
make[1]: Entering directory `/home/dct7/flappie/build'
make[2]: Entering directory `/home/dct7/flappie/build'
make[3]: Entering directory `/home/dct7/flappie/build'
make[4]: Entering directory `/home/dct7/flappie/build'
Scanning dependencies of target flappie_objects
make[4]: Leaving directory `/home/dct7/flappie/build'
make[4]: Entering directory `/home/dct7/flappie/build'
[ 7%] Building C object CMakeFiles/flappie_objects.dir/src/decode.c.o
/home/dct7/flappie/src/decode.c: In function ‘rle_trans_lookup’:
/home/dct7/flappie/src/decode.c:896:46: warning: unused parameter ‘stay_to’ [-Wunused-parameter]
size_t base_to, bool stay_to,
^~~~~~~
[ 15%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o
/home/dct7/flappie/src/layers.c: In function ‘rle_trans_lookup’:
/home/dct7/flappie/src/layers.c:1238:60: warning: unused parameter ‘stay_to’ [-Wunused-parameter]
size_t base_to, bool stay_to,
^~~~~~~
[ 23%] Building C object CMakeFiles/flappie_objects.dir/src/networks.c.o
[ 30%] Building C object CMakeFiles/flappie_objects.dir/src/nnfeatures.c.o
[ 38%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_common.c.o
[ 46%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_matrix.c.o
/home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_flappie_matrix’:
/home/dct7/flappie/src/flappie_matrix.c:150:45: warning: unused parameter ‘mat’ [-Wunused-parameter]
bool validate_flappie_matrix(flappie_matrix mat, float lower,
^~~
/home/dct7/flappie/src/flappie_matrix.c:150:56: warning: unused parameter ‘lower’ [-Wunused-parameter]
bool validate_flappie_matrix(flappie_matrix mat, float lower,
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:151:43: warning: unused parameter ‘upper’ [-Wunused-parameter]
const float upper, const float maskval,
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:151:62: warning: unused parameter ‘maskval’ [-Wunused-parameter]
const float upper, const float maskval,
^~~~~~~
/home/dct7/flappie/src/flappie_matrix.c:152:42: warning: unused parameter ‘only_finite’ [-Wunused-parameter]
const bool only_finite, const char *file,
^~~~~~~~~~~
/home/dct7/flappie/src/flappie_matrix.c:152:67: warning: unused parameter ‘file’ [-Wunused-parameter]
const bool only_finite, const char *file,
^~~~
/home/dct7/flappie/src/flappie_matrix.c:153:41: warning: unused parameter ‘line’ [-Wunused-parameter]
const int line) {
^~~~
/home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_vector’:
/home/dct7/flappie/src/flappie_matrix.c:548:29: warning: unused parameter ‘vec’ [-Wunused-parameter]
bool validate_vector(float *vec, const size_t n, const float lower,
^~~
/home/dct7/flappie/src/flappie_matrix.c:548:47: warning: unused parameter ‘n’ [-Wunused-parameter]
bool validate_vector(float *vec, const size_t n, const float lower,
^
/home/dct7/flappie/src/flappie_matrix.c:548:62: warning: unused parameter ‘lower’ [-Wunused-parameter]
bool validate_vector(float *vec, const size_t n, const float lower,
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:549:34: warning: unused parameter ‘upper’ [-Wunused-parameter]
const float upper, const char *file, const int line) {
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:549:53: warning: unused parameter ‘file’ [-Wunused-parameter]
const float upper, const char *file, const int line) {
^~~~
/home/dct7/flappie/src/flappie_matrix.c:549:69: warning: unused parameter ‘line’ [-Wunused-parameter]
const float upper, const char *file, const int line) {
^~~~
/home/dct7/flappie/src/flappie_matrix.c: In function ‘validate_ivector’:
/home/dct7/flappie/src/flappie_matrix.c:582:28: warning: unused parameter ‘vec’ [-Wunused-parameter]
bool validate_ivector(int *vec, const size_t n, const int lower, const int upper,
^~~
/home/dct7/flappie/src/flappie_matrix.c:582:46: warning: unused parameter ‘n’ [-Wunused-parameter]
bool validate_ivector(int *vec, const size_t n, const int lower, const int upper,
^
/home/dct7/flappie/src/flappie_matrix.c:582:59: warning: unused parameter ‘lower’ [-Wunused-parameter]
bool validate_ivector(int *vec, const size_t n, const int lower, const int upper,
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:582:76: warning: unused parameter ‘upper’ [-Wunused-parameter]
bool validate_ivector(int *vec, const size_t n, const int lower, const int upper,
^~~~~
/home/dct7/flappie/src/flappie_matrix.c:583:35: warning: unused parameter ‘file’ [-Wunused-parameter]
const char *file, const int line) {
^~~~
/home/dct7/flappie/src/flappie_matrix.c:583:51: warning: unused parameter ‘line’ [-Wunused-parameter]
const char *file, const int line) {
^~~~
[ 53%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_output.c.o
[ 61%] Building C object CMakeFiles/flappie_objects.dir/src/flappie_structures.c.o
[ 69%] Building C object CMakeFiles/flappie_objects.dir/src/util.c.o
make[4]: Leaving directory `/home/dct7/flappie/build'
[ 69%] Built target flappie_objects
make[4]: Entering directory `/home/dct7/flappie/build'
make[4]: Leaving directory `/home/dct7/flappie/build'
make[4]: Entering directory `/home/dct7/flappie/build'
[ 76%] Linking C static library libflappie.a
make[4]: Leaving directory `/home/dct7/flappie/build'
[ 76%] Built target flappie_static
make[4]: Entering directory `/home/dct7/flappie/build'
Scanning dependencies of target flappie
make[4]: Leaving directory `/home/dct7/flappie/build'
make[4]: Entering directory `/home/dct7/flappie/build'
[ 84%] Building C object CMakeFiles/flappie.dir/src/fast5_interface.c.o
/home/dct7/flappie/src/fast5_interface.c: In function ‘write_summary’:
/home/dct7/flappie/src/fast5_interface.c:341:16: warning: unused variable ‘status2’ [-Wunused-variable]
herr_t status2 = write_trace(read_group, trace_flat, res.trace->nr, res.trace->nc,
^~~~~~~
/home/dct7/flappie/src/fast5_interface.c:336:12: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = write_signal(read_group, res.rt.raw + res.rt.start,
^~~~~~
[ 92%] Building C object CMakeFiles/flappie.dir/src/flappie.c.o
[100%] Linking C executable flappie
CMakeFiles/flappie.dir/src/flappie.c.o: In function `main':
flappie.c:(.text.startup+0x7b6): undefined reference to `H5Fclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_float_attribute':
fast5_interface.c:(.text+0x29): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x36): undefined reference to `H5open'
fast5_interface.c:(.text+0x3d): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x4a): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x52): undefined reference to `H5Aclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5':
fast5_interface.c:(.text+0x113): undefined reference to `H5check_version'
fast5_interface.c:(.text+0x118): undefined reference to `H5open'
fast5_interface.c:(.text+0x158): undefined reference to `H5check_version'
fast5_interface.c:(.text+0x15d): undefined reference to `H5open'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `set_compression':
fast5_interface.c:(.text+0x249): undefined reference to `H5open'
fast5_interface.c:(.text+0x250): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x255): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x265): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x26f): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x27d): undefined reference to `H5Pset_chunk'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_signal':
fast5_interface.c:(.text+0x317): undefined reference to `H5Screate_simple'
fast5_interface.c:(.text+0x324): undefined reference to `H5open'
fast5_interface.c:(.text+0x32b): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x330): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x344): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x34f): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x361): undefined reference to `H5Pset_chunk'
fast5_interface.c:(.text+0x366): undefined reference to `H5open'
fast5_interface.c:(.text+0x377): undefined reference to `H5T_IEEE_F32LE_g'
fast5_interface.c:(.text+0x389): undefined reference to `H5Dcreate2'
fast5_interface.c:(.text+0x391): undefined reference to `H5open'
fast5_interface.c:(.text+0x3a0): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x3aa): undefined reference to `H5Dwrite'
fast5_interface.c:(.text+0x3b5): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0x3bd): undefined reference to `H5Pclose'
fast5_interface.c:(.text+0x3c5): undefined reference to `H5Sclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_trace':
fast5_interface.c:(.text+0x47e): undefined reference to `H5Screate_simple'
fast5_interface.c:(.text+0x48b): undefined reference to `H5open'
fast5_interface.c:(.text+0x492): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x497): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x4ab): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x4b6): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x4c8): undefined reference to `H5Pset_chunk'
fast5_interface.c:(.text+0x4cd): undefined reference to `H5open'
fast5_interface.c:(.text+0x4de): undefined reference to `H5T_STD_U8LE_g'
fast5_interface.c:(.text+0x4f0): undefined reference to `H5Dcreate2'
fast5_interface.c:(.text+0x4f8): undefined reference to `H5open'
fast5_interface.c:(.text+0x507): undefined reference to `H5T_NATIVE_INT_g'
fast5_interface.c:(.text+0x511): undefined reference to `H5Dwrite'
fast5_interface.c:(.text+0x51c): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0x524): undefined reference to `H5Pclose'
fast5_interface.c:(.text+0x52c): undefined reference to `H5Sclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_string_attribute':
fast5_interface.c:(.text+0x5b4): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x5c8): undefined reference to `H5Aget_type'
fast5_interface.c:(.text+0x5d8): undefined reference to `H5Tget_class'
fast5_interface.c:(.text+0x5f4): undefined reference to `H5Tclose'
fast5_interface.c:(.text+0x5fc): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x64c): undefined reference to `H5Tis_variable_str'
fast5_interface.c:(.text+0x65c): undefined reference to `H5Aget_space'
fast5_interface.c:(.text+0x677): undefined reference to `H5Sget_simple_extent_dims'
fast5_interface.c:(.text+0x690): undefined reference to `H5open'
fast5_interface.c:(.text+0x697): undefined reference to `H5T_C_S1_g'
fast5_interface.c:(.text+0x69c): undefined reference to `H5Tcopy'
fast5_interface.c:(.text+0x6ae): undefined reference to `H5Tset_size'
fast5_interface.c:(.text+0x6be): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x6ce): undefined reference to `H5Tclose'
fast5_interface.c:(.text+0x6d6): undefined reference to `H5Sclose'
fast5_interface.c:(.text+0x6e4): undefined reference to `H5Tget_size'
fast5_interface.c:(.text+0x705): undefined reference to `H5Aread'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `get_raw_scaling':
fast5_interface.c:(.text+0x7d4): undefined reference to `H5Gopen2'
fast5_interface.c:(.text+0x7f7): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x808): undefined reference to `H5open'
fast5_interface.c:(.text+0x80f): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x81c): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x824): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x846): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x857): undefined reference to `H5open'
fast5_interface.c:(.text+0x85e): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x86b): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x873): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x895): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x8a6): undefined reference to `H5open'
fast5_interface.c:(.text+0x8ad): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x8ba): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x8c2): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x8e4): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x8f5): undefined reference to `H5open'
fast5_interface.c:(.text+0x8fc): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x909): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x911): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x91d): undefined reference to `H5Gclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_raw':
fast5_interface.c:(.text+0xa78): undefined reference to `H5check_version'
fast5_interface.c:(.text+0xa7d): undefined reference to `H5open'
fast5_interface.c:(.text+0xa89): undefined reference to `H5Fopen'
fast5_interface.c:(.text+0xaa0): undefined reference to `H5Eset_auto2'
fast5_interface.c:(.text+0xabb): undefined reference to `H5Lget_name_by_idx'
fast5_interface.c:(.text+0xafc): undefined reference to `H5Lget_name_by_idx'
fast5_interface.c:(.text+0xb33): undefined reference to `H5Gopen2'
fast5_interface.c:(.text+0xb5f): undefined reference to `H5Gclose'
fast5_interface.c:(.text+0xb9b): undefined reference to `H5Dopen2'
fast5_interface.c:(.text+0xbb1): undefined reference to `H5Dget_space'
fast5_interface.c:(.text+0xbce): undefined reference to `H5Sget_simple_extent_dims'
fast5_interface.c:(.text+0xbe5): undefined reference to `H5open'
fast5_interface.c:(.text+0xbf6): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0xc00): undefined reference to `H5Dread'
fast5_interface.c:(.text+0xc28): undefined reference to `H5Sclose'
fast5_interface.c:(.text+0xc32): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0xc7c): undefined reference to `H5Fclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary':
fast5_interface.c:(.text+0x109c): undefined reference to `H5Gcreate2'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5':
fast5_interface.c:(.text+0x13e): undefined reference to `H5Fcreate'
fast5_interface.c:(.text+0x181): undefined reference to `H5Fopen'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `create_group':
fast5_interface.c:(.text+0x1f0): undefined reference to `H5Gcreate2'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary':
fast5_interface.c:(.text+0x111d): undefined reference to `H5Gclose'
collect2: error: ld returned 1 exit status
make[4]: *** [flappie] Error 1
make[4]: Leaving directory `/home/dct7/flappie/build'
make[3]: *** [CMakeFiles/flappie.dir/all] Error 2
make[3]: Leaving directory `/home/dct7/flappie/build'
make[2]: *** [CMakeFiles/flappie.dir/rule] Error 2
make[2]: Leaving directory `/home/dct7/flappie/build'
make[1]: *** [flappie] Error 2
make[1]: Leaving directory `/home/dct7/flappie/build'
make: *** [build/flappie] Error 2
flappie hdf5.h error
Hi I am trying to install flappie in ubuntu 18.04 and when i do make flappie i am getting the following errors , I have all my dependencies installed already
cd build &&
cmake .. -DCMAKE_BUILD_TYPE=Release -DHDF5_ROOT='' &&
make flappie
-- Configuring done
-- Generating done
-- Build files have been written to: /home/madhu/flappie/build
make[1]: Entering directory '/home/madhu/flappie/build'
make[2]: Entering directory '/home/madhu/flappie/build'
make[3]: Entering directory '/home/madhu/flappie/build'
make[4]: Entering directory '/home/madhu/flappie/build'
make[4]: Leaving directory '/home/madhu/flappie/build'
[ 84%] Built target flappie_objects
make[4]: Entering directory '/home/madhu/flappie/build'
make[4]: Leaving directory '/home/madhu/flappie/build'
[ 84%] Built target flappie_static
make[4]: Entering directory '/home/madhu/flappie/build'
make[4]: Leaving directory '/home/madhu/flappie/build'
make[4]: Entering directory '/home/madhu/flappie/build'
[ 84%] Building C object CMakeFiles/flappie.dir/src/fast5_interface.c.o
cc1: warning: /usr/include/hdf5/serial/hdf5.h: not a directory
In file included from /home/madhu/flappie/src/fast5_interface.c:21:0:
/home/madhu/flappie/src/fast5_interface.h:13:10: fatal error: hdf5.h: No such file or directory
#include <hdf5.h>
^~~~~~~~
compilation terminated.
CMakeFiles/flappie.dir/build.make:62: recipe for target 'CMakeFiles/flappie.dir/src/fast5_interface.c.o' failed
make[4]: *** [CMakeFiles/flappie.dir/src/fast5_interface.c.o] Error 1
make[4]: Leaving directory '/home/madhu/flappie/build'
CMakeFiles/Makefile2:141: recipe for target 'CMakeFiles/flappie.dir/all' failed
make[3]: *** [CMakeFiles/flappie.dir/all] Error 2
make[3]: Leaving directory '/home/madhu/flappie/build'
CMakeFiles/Makefile2:153: recipe for target 'CMakeFiles/flappie.dir/rule' failed
make[2]: *** [CMakeFiles/flappie.dir/rule] Error 2
make[2]: Leaving directory '/home/madhu/flappie/build'
Makefile:223: recipe for target 'flappie' failed
make[1]: *** [flappie] Error 2
make[1]: Leaving directory '/home/madhu/flappie/build'
Makefile:30: recipe for target 'build/flappie' failed
make: *** [build/flappie] Error 2
Help me in fixing the error. Thanks in advance
batch response: Git LFS is disabled for this repository.
Cloning into 'flappie'...
remote: Enumerating objects: 107, done.
remote: Counting objects: 100% (107/107), done.
remote: Compressing objects: 100% (76/76), done.
remote: Total 491 (delta 58), reused 63 (delta 29), pack-reused 384
Receiving objects: 100% (491/491), 8.24 MiB | 1.63 MiB/s, done.
Resolving deltas: 100% (284/284), done.
Downloading reads/MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5 (2.1 MB)
Error downloading object: reads/MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5 (105bdea): Smudge error: Error downloading reads/MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5 (105bdeadfc8fbfb064f0c4176ae9a1df0f028191d64e98d9ff9408d3ab65b7a5): batch response: Git LFS is disabled for this repository.
Errors logged to /Users/quanc/Documents/Workspace/Github/flappie/.git/lfs/logs/20190125T160843.080186.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: reads/MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch174_read172_strand.fast5: smudge filter lfs failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'
Git LFS "This repository is over its data quota."
Cloning into 'flappie'...
remote: Enumerating objects: 169, done.
remote: Counting objects: 100% (169/169), done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 667 (delta 98), reused 140 (delta 79), pack-reused 498
Receiving objects: 100% (667/667), 8.28 MiB | 10.42 MiB/s, done.
Resolving deltas: 100% (402/402), done.
Downloading reads/multi/FAK40126_2fd3b110ca0d020049836a61f0dfb2b9983808f9_0.fast5 (206 KB)
Error downloading object: reads/multi/FAK40126_2fd3b110ca0d020049836a61f0dfb2b9983808f9_0.fast5 (43d19c3): Smudge error: Error downloading reads/multi/FAK40126_2fd3b110ca0d020049836a61f0dfb2b9983808f9_0.fast5 (43d19c30b6463226f1e6e9a5eeb288ae567207158826013d352881d8e49bc0ef): batch response: This repository is over its data quota. Purchase more data packs to restore access.
Errors logged to /Users/jordisr/software/flappie/.git/lfs/logs/20190923T131943.872757.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: reads/multi/FAK40126_2fd3b110ca0d020049836a61f0dfb2b9983808f9_0.fast5: smudge filter lfs failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'
Doesn't look like any of the models in src/models were downloaded either.
kmer model
Hi,
It suggests that flappie has separate models (r941_native and r941mC_native) for R9.4 MinION and PromethION flow cell. Can you please let me know if there is a way to extract the kmer model from this (with the mean and standard deviation of the current values corresponding to each kmer)?
Thank you,
Dhaivat
misc/decode_runnie.py:57: RuntimeWarning: invalid value encountered in log1p return np.exp(y * np.log1p(x))
Hi Tim,
I seem to be getting this error when running runnie. Any suggestions?
python3 misc/decode_runnie.py run12.run > Run12_runnie_basecalls.fa misc/decode_runnie.py:57: RuntimeWarning: invalid value encountered in log1p return np.exp(y * np.log1p(x)) misc/decode_runnie.py:51: RuntimeWarning: invalid value encountered in power a = np.power((x - 1) / scale, shape) misc/decode_runnie.py:74: RuntimeWarning: invalid value encountered in greater run_mode = np.where((run_mode > 1) & (pmf_mode_m1 > pmf_mode), misc/decode_runnie.py:57: RuntimeWarning: divide by zero encountered in log1p return np.exp(y * np.log1p(x)) misc/decode_runnie.py:57: RuntimeWarning: invalid value encountered in log1p return np.exp(y * np.log1p(x)) misc/decode_runnie.py:51: RuntimeWarning: invalid value encountered in power a = np.power((x - 1) / scale, shape) misc/decode_runnie.py:74: RuntimeWarning: invalid value encountered in greater run_mode = np.where((run_mode > 1) & (pmf_mode_m1 > pmf_mode), misc/decode_runnie.py:57: RuntimeWarning: divide by zero encountered in log1p return np.exp(y * np.log1p(x)) misc/decode_runnie.py:86: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison base_vec[base_vec == b] = i
how do you label the raw signal sequence with nucleotides
Hi:
how do you label the raw signal sequence with nucleotides for training dataset?
Error when install flappie
Hi,
I tried to install flappie with
LDFLAGS="-L/home/801/ww2693/xf1/devel/python/anaconda3/lib" CFLAGS="-I/home/801/ww2693/xf1/devel/python/anaconda3/include" make flappie
And then I got this error
mkdir build
cd build && \
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DHDF5_ROOT='' \
-DOPENBLAS_REDHAT='' \
-DOPENBLAS_ROOT='' && \
make flappie
-- The C compiler identification is GNU 4.4.7
-- Check for working C compiler: /opt/bin/cc
-- Check for working C compiler: /opt/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for hdf5.h
-- Looking for hdf5.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/801/ww2693/xf1/devel/flappie/build
make[1]: Entering directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[2]: Entering directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[3]: Entering directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[4]: Entering directory `/g/data1a/xf1/raymond/devel/flappie/build'
Scanning dependencies of target flappie_objects
make[4]: Leaving directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[4]: Entering directory `/g/data1a/xf1/raymond/devel/flappie/build'
[ 7%] Building C object CMakeFiles/flappie_objects.dir/src/decode.c.o
/home/801/ww2693/xf1/devel/flappie/src/decode.c: In function 'rle_trans_lookup':
/home/801/ww2693/xf1/devel/flappie/src/decode.c:896: warning: unused parameter 'stay_to'
[ 15%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o
/home/801/ww2693/xf1/devel/flappie/src/layers.c: In function 'rle_trans_lookup':
/home/801/ww2693/xf1/devel/flappie/src/layers.c:1238: warning: unused parameter 'stay_to'
[ 23%] Building C object CMakeFiles/flappie_objects.dir/src/networks.c.o
In file included from /home/801/ww2693/xf1/devel/flappie/src/networks.c:10:
/home/801/ww2693/xf1/devel/flappie/src/models/flipflop_r941native.h:1: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'https'
In file included from /home/801/ww2693/xf1/devel/flappie/src/networks.c:10:
/home/801/ww2693/xf1/devel/flappie/src/models/flipflop_r941native.h:2:12: error: invalid suffix "dd6adb73a55d95014a6701658d399069b144451dff9179cbefbfb39bb230e" on integer constant
In file included from /home/801/ww2693/xf1/devel/flappie/src/networks.c:11:
/home/801/ww2693/xf1/devel/flappie/src/models/flipflop_r941native5mC.h:2:12: error: invalid suffix "bffdb61b0389174ce2be46ff2e41ae9efaf1332fef6638b8b8e41cf67838" on integer constant
In file included from /home/801/ww2693/xf1/devel/flappie/src/networks.c:13:
/home/801/ww2693/xf1/devel/flappie/src/models/runlength_r941native.h:2:12: error: invalid suffix "b5a87f97b742bcda448ef8be537afce64a1624a73ffd83807808cfda5423fe" on integer constant
In file included from /home/801/ww2693/xf1/devel/flappie/src/networks.c:14:
/home/801/ww2693/xf1/devel/flappie/src/models/runlength_r941nativeV2.h:2:12: error: invalid suffix "a9fd5042ca17f2f52be2da8dd9056b398d048f55b0cb7973af376e31a61218" on integer constant
/home/801/ww2693/xf1/devel/flappie/src/networks.c:183: error: '_conv_rnnrf_flipflop_r941native_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:184: error: '_conv_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:185: error: 'conv_rnnrf_flipflop_r941native_stride' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:188: error: '_gruB1_rnnrf_flipflop_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:189: error: '_gruB1_rnnrf_flipflop_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:190: error: '_gruB1_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:192: error: '_gruF2_rnnrf_flipflop_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:193: error: '_gruF2_rnnrf_flipflop_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:194: error: '_gruF2_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:196: error: '_gruB3_rnnrf_flipflop_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:197: error: '_gruB3_rnnrf_flipflop_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:198: error: '_gruB3_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:200: error: '_gruF4_rnnrf_flipflop_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:201: error: '_gruF4_rnnrf_flipflop_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:202: error: '_gruF4_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:204: error: '_gruB5_rnnrf_flipflop_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:205: error: '_gruB5_rnnrf_flipflop_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:206: error: '_gruB5_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:208: error: '_FF_rnnrf_flipflop_r941native_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:209: error: '_FF_rnnrf_flipflop_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:215: error: '_conv_rnnrf_flipflop_r941native5mC_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:216: error: '_conv_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:217: error: 'conv_rnnrf_flipflop_r941native5mC_stride' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:220: error: '_gruB1_rnnrf_flipflop_r941native5mC_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:221: error: '_gruB1_rnnrf_flipflop_r941native5mC_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:222: error: '_gruB1_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:224: error: '_gruF2_rnnrf_flipflop_r941native5mC_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:225: error: '_gruF2_rnnrf_flipflop_r941native5mC_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:226: error: '_gruF2_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:228: error: '_gruB3_rnnrf_flipflop_r941native5mC_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:229: error: '_gruB3_rnnrf_flipflop_r941native5mC_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:230: error: '_gruB3_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:232: error: '_gruF4_rnnrf_flipflop_r941native5mC_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:233: error: '_gruF4_rnnrf_flipflop_r941native5mC_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:234: error: '_gruF4_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:236: error: '_gruB5_rnnrf_flipflop_r941native5mC_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:237: error: '_gruB5_rnnrf_flipflop_r941native5mC_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:238: error: '_gruB5_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:240: error: '_FF_rnnrf_flipflop_r941native5mC_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:241: error: '_FF_rnnrf_flipflop_r941native5mC_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:247: error: '_conv_rnnrf_flipflop_r10Cpcr_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:248: error: '_conv_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:249: error: 'conv_rnnrf_flipflop_r10Cpcr_stride' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:252: error: '_gruB1_rnnrf_flipflop_r10Cpcr_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:253: error: '_gruB1_rnnrf_flipflop_r10Cpcr_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:254: error: '_gruB1_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:256: error: '_gruF2_rnnrf_flipflop_r10Cpcr_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:257: error: '_gruF2_rnnrf_flipflop_r10Cpcr_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:258: error: '_gruF2_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:260: error: '_gruB3_rnnrf_flipflop_r10Cpcr_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:261: error: '_gruB3_rnnrf_flipflop_r10Cpcr_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:262: error: '_gruB3_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:264: error: '_gruF4_rnnrf_flipflop_r10Cpcr_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:265: error: '_gruF4_rnnrf_flipflop_r10Cpcr_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:266: error: '_gruF4_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:268: error: '_gruB5_rnnrf_flipflop_r10Cpcr_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:269: error: '_gruB5_rnnrf_flipflop_r10Cpcr_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:270: error: '_gruB5_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:272: error: '_FF_rnnrf_flipflop_r10Cpcr_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:273: error: '_FF_rnnrf_flipflop_r10Cpcr_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:279: error: '_conv_runlength_r941native_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:280: error: '_conv_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:281: error: 'conv_runlength_r941native_stride' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:284: error: '_gruB1_runlength_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:285: error: '_gruB1_runlength_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:286: error: '_gruB1_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:288: error: '_gruF2_runlength_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:289: error: '_gruF2_runlength_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:290: error: '_gruF2_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:292: error: '_gruB3_runlength_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:293: error: '_gruB3_runlength_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:294: error: '_gruB3_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:296: error: '_gruF4_runlength_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:297: error: '_gruF4_runlength_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:298: error: '_gruF4_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:300: error: '_gruB5_runlength_r941native_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:301: error: '_gruB5_runlength_r941native_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:302: error: '_gruB5_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:304: error: '_FF_runlength_r941native_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:305: error: '_FF_runlength_r941native_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:310: error: '_conv_rnnrf_rle_r941nativeV2_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:311: error: '_conv_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:312: error: 'conv_rnnrf_rle_r941nativeV2_stride' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:315: error: '_gruB1_rnnrf_rle_r941nativeV2_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:316: error: '_gruB1_rnnrf_rle_r941nativeV2_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:317: error: '_gruB1_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:319: error: '_gruF2_rnnrf_rle_r941nativeV2_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:320: error: '_gruF2_rnnrf_rle_r941nativeV2_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:321: error: '_gruF2_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:323: error: '_gruB3_rnnrf_rle_r941nativeV2_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:324: error: '_gruB3_rnnrf_rle_r941nativeV2_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:325: error: '_gruB3_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:327: error: '_gruF4_rnnrf_rle_r941nativeV2_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:328: error: '_gruF4_rnnrf_rle_r941nativeV2_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:329: error: '_gruF4_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:331: error: '_gruB5_rnnrf_rle_r941nativeV2_iW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:332: error: '_gruB5_rnnrf_rle_r941nativeV2_sW' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:333: error: '_gruB5_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:335: error: '_FF_rnnrf_rle_r941nativeV2_W' undeclared here (not in a function)
/home/801/ww2693/xf1/devel/flappie/src/networks.c:336: error: '_FF_rnnrf_rle_r941nativeV2_b' undeclared here (not in a function)
make[4]: *** [CMakeFiles/flappie_objects.dir/src/networks.c.o] Error 1
make[4]: Leaving directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[3]: *** [CMakeFiles/flappie_objects.dir/all] Error 2
make[3]: Leaving directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[2]: *** [CMakeFiles/flappie.dir/rule] Error 2
make[2]: Leaving directory `/g/data1a/xf1/raymond/devel/flappie/build'
make[1]: *** [flappie] Error 2
make[1]: Leaving directory `/g/data1a/xf1/raymond/devel/flappie/build'
make: *** [build/flappie] Error 2
It seems that it is related to Git LFS missing in FAQs, but I have installed git-lfs-2.8.0 with conda.
flappie: Failed find read name under /Raw/Reads/
Hello,
Hi,
when trying to basecall Fast5 files I get the following error:
flappie: Failed find read name under /Raw/Reads/
flappie: No basecall returned for ...
The data come directly from the MinION. I checked the files and they seem correct.
Using the HDFView tool, I checked that the reads have names.
Does anyone have an idea how to fix this error?
Greetings
what about barcoding
Dear,
i was wondering if flappie will have an option like in Albacore to de-barcode mixed run.
thanks
Luigi
Methylation in SAM
I started investigations into how to store such data in SAM. It's non trivial due to BAM's choice of using nibbles to store sequences, thus uppercase bases + ambiguity codes are the only choices available.
The actual storage method hasn't been finalised yet, and frankly I'm in the deep end with this anyway so it's a learning experience for me too. However I have done some experiments, both actual data compression and thought based, on which methods work well.
One key thing to consider is that applications may not be methylation aware. If we are doing sequence alignment or homology computation, we don't want to treat methylated C as an N for scoring purposes, but you can bet this is what 99% of software will do. Therefore a side channel, with the "fundamental" base in the SAM SEQuence field and the modification status in an auxiliary tag, looks like the sensible way to go.
This is the time for the community to be making suggestions so we can come up with an appriopriate hts-specs update.
Issue when Make on ubuntu 18.04
Download git clone after installing git-lfs
Proceed to make flappie and get following error
`
make flappie
cd build &&
cmake .. -DCMAKE_BUILD_TYPE=Release
-DHDF5_ROOT=''
-DOPENBLAS_REDHAT=''
-DOPENBLAS_ROOT='' &&
make flappie
-- Configuring done
-- Generating done
-- Build files have been written to: /home/minion/flappie/build
make[1]: Entering directory '/home/minion/flappie/build'
make[2]: Entering directory '/home/minion/flappie/build'
make[3]: Entering directory '/home/minion/flappie/build'
make[4]: Entering directory '/home/minion/flappie/build'
make[4]: Leaving directory '/home/minion/flappie/build'
make[4]: Entering directory '/home/minion/flappie/build'
[ 7%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o
/home/minion/flappie/src/layers.c:12:14: fatal error: cblas.h: No such file or directory
include <cblas.h>
^~~~~~~~~
compilation terminated.
make[4]: *** [CMakeFiles/flappie_objects.dir/build.make:87: CMakeFiles/flappie_objects.dir/src/layers.c.o] Error 1
make[4]: Leaving directory '/home/minion/flappie/build'
make[3]: *** [CMakeFiles/Makefile2:105: CMakeFiles/flappie_objects.dir/all] Error 2
make[3]: Leaving directory '/home/minion/flappie/build'
make[2]: *** [CMakeFiles/Makefile2:154: CMakeFiles/flappie.dir/rule] Error 2
make[2]: Leaving directory '/home/minion/flappie/build'
make[1]: *** [Makefile:223: flappie] Error 2
make[1]: Leaving directory '/home/minion/flappie/build'
make: *** [Makefile:36: build/flappie] Error 2
`
I repeated install of dependencies and I think cblas.h is correctly situated in the /usr/include directory.
I had similar issues on ubuntu 16.04 after installing all dependencies I checked the files in /usr/include and it fails to find files from hdf5. This seems because they are placed in subdirectory /usr/include/hdf5/serial/.....
I created sym links for these into /usr/include/ and make progresses but then throws error.
cd build && \
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DHDF5_ROOT='' \
-DOPENBLAS_REDHAT='' \
-DOPENBLAS_ROOT='' && \
make flappie
-- Configuring done
-- Generating done
-- Build files have been written to: /flappie/build
make[1]: Entering directory '/flappie/build'
make[2]: Entering directory '/flappie/build'
make[3]: Entering directory '/flappie/build'
make[4]: Entering directory '/flappie/build'
make[4]: Leaving directory '/flappie/build'
[ 69%] Built target flappie_objects
make[4]: Entering directory '/flappie/build'
make[4]: Leaving directory '/flappie/build'
[ 76%] Built target flappie_static
make[4]: Entering directory '/flappie/build'
make[4]: Leaving directory '/flappie/build'
make[4]: Entering directory '/flappie/build'
[ 84%] Building C object CMakeFiles/flappie.dir/src/fast5_interface.c.o
/flappie/src/fast5_interface.c: In function 'write_summary':
/flappie/src/fast5_interface.c:341:16: warning: unused variable 'status2' [-Wunused-variable]
herr_t status2 = write_trace(read_group, trace_flat, res.trace->nr, res.trace->nc,
^
/flappie/src/fast5_interface.c:336:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = write_signal(read_group, res.rt.raw + res.rt.start,
^
[ 92%] Building C object CMakeFiles/flappie.dir/src/flappie.c.o
[100%] Linking C executable flappie
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_float_attribute':
fast5_interface.c:(.text+0x28): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x33): undefined reference to `H5open'
fast5_interface.c:(.text+0x39): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x45): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x4c): undefined reference to `H5Aclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5':
fast5_interface.c:(.text+0x103): undefined reference to `H5check_version'
fast5_interface.c:(.text+0x140): undefined reference to `H5check_version'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `set_compression':
fast5_interface.c:(.text+0x219): undefined reference to `H5open'
fast5_interface.c:(.text+0x21f): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x224): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x231): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x23a): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x247): undefined reference to `H5Pset_chunk'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_signal':
fast5_interface.c:(.text+0x2e2): undefined reference to `H5Screate_simple'
fast5_interface.c:(.text+0x2ef): undefined reference to `H5open'
fast5_interface.c:(.text+0x2f5): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x2fa): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x30b): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x315): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x326): undefined reference to `H5Pset_chunk'
fast5_interface.c:(.text+0x32b): undefined reference to `H5open'
fast5_interface.c:(.text+0x33a): undefined reference to `H5T_IEEE_F32LE_g'
fast5_interface.c:(.text+0x34c): undefined reference to `H5Dcreate2'
fast5_interface.c:(.text+0x354): undefined reference to `H5open'
fast5_interface.c:(.text+0x35a): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x36c): undefined reference to `H5Dwrite'
fast5_interface.c:(.text+0x376): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0x37d): undefined reference to `H5Pclose'
fast5_interface.c:(.text+0x385): undefined reference to `H5Sclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_trace':
fast5_interface.c:(.text+0x439): undefined reference to `H5Screate_simple'
fast5_interface.c:(.text+0x446): undefined reference to `H5open'
fast5_interface.c:(.text+0x44c): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
fast5_interface.c:(.text+0x451): undefined reference to `H5Pcreate'
fast5_interface.c:(.text+0x462): undefined reference to `H5Pset_shuffle'
fast5_interface.c:(.text+0x46c): undefined reference to `H5Pset_deflate'
fast5_interface.c:(.text+0x47d): undefined reference to `H5Pset_chunk'
fast5_interface.c:(.text+0x482): undefined reference to `H5open'
fast5_interface.c:(.text+0x491): undefined reference to `H5T_STD_U8LE_g'
fast5_interface.c:(.text+0x4a3): undefined reference to `H5Dcreate2'
fast5_interface.c:(.text+0x4ab): undefined reference to `H5open'
fast5_interface.c:(.text+0x4b1): undefined reference to `H5T_NATIVE_INT_g'
fast5_interface.c:(.text+0x4c3): undefined reference to `H5Dwrite'
fast5_interface.c:(.text+0x4cd): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0x4d4): undefined reference to `H5Pclose'
fast5_interface.c:(.text+0x4dc): undefined reference to `H5Sclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_string_attribute':
fast5_interface.c:(.text+0x563): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x574): undefined reference to `H5Aget_type'
fast5_interface.c:(.text+0x581): undefined reference to `H5Tget_class'
fast5_interface.c:(.text+0x59c): undefined reference to `H5Tclose'
fast5_interface.c:(.text+0x5a3): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x5eb): undefined reference to `H5Tis_variable_str'
fast5_interface.c:(.text+0x5fa): undefined reference to `H5Aget_space'
fast5_interface.c:(.text+0x614): undefined reference to `H5Sget_simple_extent_dims'
fast5_interface.c:(.text+0x62d): undefined reference to `H5open'
fast5_interface.c:(.text+0x633): undefined reference to `H5T_C_S1_g'
fast5_interface.c:(.text+0x638): undefined reference to `H5Tcopy'
fast5_interface.c:(.text+0x649): undefined reference to `H5Tset_size'
fast5_interface.c:(.text+0x657): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x667): undefined reference to `H5Tclose'
fast5_interface.c:(.text+0x66f): undefined reference to `H5Sclose'
fast5_interface.c:(.text+0x683): undefined reference to `H5Tget_size'
fast5_interface.c:(.text+0x6a2): undefined reference to `H5Aread'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `get_raw_scaling':
fast5_interface.c:(.text+0x764): undefined reference to `H5Gopen2'
fast5_interface.c:(.text+0x784): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x793): undefined reference to `H5open'
fast5_interface.c:(.text+0x799): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x7a5): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x7ac): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x7cd): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x7dc): undefined reference to `H5open'
fast5_interface.c:(.text+0x7e2): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x7ee): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x7f5): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x816): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x825): undefined reference to `H5open'
fast5_interface.c:(.text+0x82b): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x837): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x83e): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x85f): undefined reference to `H5Aopen'
fast5_interface.c:(.text+0x86e): undefined reference to `H5open'
fast5_interface.c:(.text+0x874): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0x880): undefined reference to `H5Aread'
fast5_interface.c:(.text+0x887): undefined reference to `H5Aclose'
fast5_interface.c:(.text+0x898): undefined reference to `H5Gclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `read_raw':
fast5_interface.c:(.text+0xa08): undefined reference to `H5check_version'
fast5_interface.c:(.text+0xa14): undefined reference to `H5Fopen'
fast5_interface.c:(.text+0xa2a): undefined reference to `H5Eset_auto2'
fast5_interface.c:(.text+0xa45): undefined reference to `H5Lget_name_by_idx'
fast5_interface.c:(.text+0xa88): undefined reference to `H5Lget_name_by_idx'
fast5_interface.c:(.text+0xad2): undefined reference to `H5Gopen2'
fast5_interface.c:(.text+0xafb): undefined reference to `H5Gclose'
fast5_interface.c:(.text+0xb47): undefined reference to `H5Dopen2'
fast5_interface.c:(.text+0xb5b): undefined reference to `H5Dget_space'
fast5_interface.c:(.text+0xb73): undefined reference to `H5Sget_simple_extent_dims'
fast5_interface.c:(.text+0xb89): undefined reference to `H5open'
fast5_interface.c:(.text+0xb8f): undefined reference to `H5T_NATIVE_FLOAT_g'
fast5_interface.c:(.text+0xba1): undefined reference to `H5Dread'
fast5_interface.c:(.text+0xbc3): undefined reference to `H5Sclose'
fast5_interface.c:(.text+0xbcb): undefined reference to `H5Dclose'
fast5_interface.c:(.text+0xc13): undefined reference to `H5Fclose'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary':
fast5_interface.c:(.text+0x110b): undefined reference to `H5Gcreate2'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `open_or_create_hdf5':
fast5_interface.c:(.text+0x129): undefined reference to `H5Fcreate'
fast5_interface.c:(.text+0x164): undefined reference to `H5Fopen'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `create_group':
fast5_interface.c:(.text+0x1cc): undefined reference to `H5Gcreate2'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_summary':
fast5_interface.c:(.text+0x118b): undefined reference to `H5Gclose'
CMakeFiles/flappie.dir/src/flappie.c.o: In function `main':
flappie.c:(.text.startup+0x7b9): undefined reference to `H5Fclose'
collect2: error: ld returned 1 exit status
CMakeFiles/flappie.dir/build.make:121: recipe for target 'flappie' failed
make[4]: *** [flappie] Error 1
make[4]: Leaving directory '/flappie/build'
CMakeFiles/Makefile2:173: recipe for target 'CMakeFiles/flappie.dir/all' failed
make[3]: *** [CMakeFiles/flappie.dir/all] Error 2
make[3]: Leaving directory '/flappie/build'
CMakeFiles/Makefile2:185: recipe for target 'CMakeFiles/flappie.dir/rule' failed
make[2]: *** [CMakeFiles/flappie.dir/rule] Error 2
make[2]: Leaving directory '/flappie/build'
Makefile:234: recipe for target 'flappie' failed
make[1]: *** [flappie] Error 2
make[1]: Leaving directory '/flappie/build'
Makefile:36: recipe for target 'build/flappie' failed
make: *** [build/flappie] Error 2
How to set qscore offset and scaling when using novel model from taiyaki?
The choice between ACGT and ACGU should not matter, as long as the alphabet used for prepare_mapped_reads.py is consistent with the per-read references you provide (i.e. if you use Ts in the references then use ACGT).
The accuracy of the basecalls is much better than the Q-scores imply, which indicates a problem with the calibration of the Q-scores. We don't calculate Q-scores in taiyaki, this is only done in guppy, so I'm afraid I don't know exactly why this could happen.
I note however that guppy applies a shift and scale to the Q-scores, and these seem to be different for each model. If you ask on the community you may get an answer from the guppy devs about how these are determined. In the meantime you can adjust these with the command line arguments for guppy: --qscore_offset and --qscore_scale, or you can adjust the pass/fail cutoff with --min_qscore.
Originally posted by @myrtlecat in nanoporetech/taiyaki#53 (comment)
This is in reference to my posted issue on taiyaki issue board
OpenBLAS not found
Hi,
Can you please provide the option to specify path to OpenBLAS include and library directory via cmake variable ?
I am trying to build flappie and it always fails with the error message:
/scratch/85150120.tmpdir/flappie/src/fast5_interface.c:336:12: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = write_signal(read_group, res.rt.raw + res.rt.start,
^
[ 52%] Building C object CMakeFiles/flappie.dir/src/flappie.c.o
[ 56%] Linking C executable flappie
/usr/bin/ld: cannot find -lblas
Even if I set $OPENBLAS_ROOT, flappie will still try to link with -lblas
Best regards
Sam
minimizing memory requirement
Hello Tim,
I am looking for suggestions to minimize the memory requirement of flappie as I am trying to map it to FPGA based accelerator.
Particularly the input feature vector for each read need to be processed as a whole by the network. The size of the feature vector can range from few hundred MB to couple of GBs. depending on the size of fast5 file being processed. Is it possible to run the neural network on a fixed sliding window, overlapping the sequences on these windows and generating consensus. Similar to what for example Chiron does.
Thanks,
Ram
running flappie on ubuntu 18.04
im following the instructions for 16.04 for 18.04 as well,
Running
libcunit1
libhdf5
libopenblas-base
Building
cmake
libcunit1-dev
libhdf5-dev
libopenblas-dev
But i cant seem to figure out how to install libhdf5.
tried this as well,
sudo apt-get install libhdf5-serial-dev
Installation got stuck in the middle
while i was trying to run flappie after installing the python modules and other dependencies, i got stuck in middle which is attached below as snapshot. Please help me in sorting out this issue.Thanks
model without zero padding
Hello,
The convolution model in the model file, looks to be padded with zeroes. I am guessing it is for enabling vectorization by aligning with 128bits boundary. Is this understanding correct or is there any other reason for it?
I was looking for a an mdl file without zero padding. Please let me know if any such models are available.
Thank you,
Ram
Compilation errors: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘https’ In file included from networks.c:10:
Hi flappie community,
I'm getting compilation errors:
make flappie
mkdir build
cd build &&
cmake .. -DCMAKE_BUILD_TYPE=Release &&
make
-- The C compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for hdf5.h
-- Looking for hdf5.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /projects/li-lab/software/flappie/build
make[1]: Entering directory /projects/li-lab/software/flappie/build' make[2]: Entering directory /projects/li-lab/software/flappie/build'
make[3]: Entering directory /projects/li-lab/software/flappie/build' Scanning dependencies of target flappie_objects make[3]: Leaving directory /projects/li-lab/software/flappie/build'
make[3]: Entering directory /projects/li-lab/software/flappie/build' [ 4%] Building C object CMakeFiles/flappie_objects.dir/src/decode.c.o [ 8%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o [ 13%] Building C object CMakeFiles/flappie_objects.dir/src/networks.c.o In file included from /projects/li-lab/software/flappie/src/networks.c:10: /projects/li-lab/software/flappie/src/models/flipflop_r941native.h:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘https’ In file included from /projects/li-lab/software/flappie/src/networks.c:10: /projects/li-lab/software/flappie/src/models/flipflop_r941native.h:2:12: error: invalid suffix "dd6adb73a55d95014a6701658d399069b144451dff9179cbefbfb39bb230e" on integer constant In file included from /projects/li-lab/software/flappie/src/networks.c:11: /projects/li-lab/software/flappie/src/models/flipflop_r941native5mC.h:2:12: error: invalid suffix "bffdb61b0389174ce2be46ff2e41ae9efaf1332fef6638b8b8e41cf67838" on integer constant /projects/li-lab/software/flappie/src/networks.c:160: error: ‘_conv_rnnrf_flipflop_r941native_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:161: error: ‘_conv_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:162: error: ‘conv_rnnrf_flipflop_r941native_stride’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:165: error: ‘_gruB1_rnnrf_flipflop_r941native_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:166: error: ‘_gruB1_rnnrf_flipflop_r941native_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:167: error: ‘_gruB1_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:169: error: ‘_gruF2_rnnrf_flipflop_r941native_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:170: error: ‘_gruF2_rnnrf_flipflop_r941native_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:171: error: ‘_gruF2_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:173: error: ‘_gruB3_rnnrf_flipflop_r941native_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:174: error: ‘_gruB3_rnnrf_flipflop_r941native_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:175: error: ‘_gruB3_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:177: error: ‘_gruF4_rnnrf_flipflop_r941native_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:178: error: ‘_gruF4_rnnrf_flipflop_r941native_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:179: error: ‘_gruF4_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:181: error: ‘_gruB5_rnnrf_flipflop_r941native_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:182: error: ‘_gruB5_rnnrf_flipflop_r941native_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:183: error: ‘_gruB5_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:185: error: ‘_FF_rnnrf_flipflop_r941native_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:186: error: ‘_FF_rnnrf_flipflop_r941native_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:192: error: ‘_conv_rnnrf_flipflop_r941native5mC_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:193: error: ‘_conv_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:194: error: ‘conv_rnnrf_flipflop_r941native5mC_stride’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:197: error: ‘_gruB1_rnnrf_flipflop_r941native5mC_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:198: error: ‘_gruB1_rnnrf_flipflop_r941native5mC_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:199: error: ‘_gruB1_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:201: error: ‘_gruF2_rnnrf_flipflop_r941native5mC_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:202: error: ‘_gruF2_rnnrf_flipflop_r941native5mC_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:203: error: ‘_gruF2_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:205: error: ‘_gruB3_rnnrf_flipflop_r941native5mC_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:206: error: ‘_gruB3_rnnrf_flipflop_r941native5mC_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:207: error: ‘_gruB3_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:209: error: ‘_gruF4_rnnrf_flipflop_r941native5mC_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:210: error: ‘_gruF4_rnnrf_flipflop_r941native5mC_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:211: error: ‘_gruF4_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:213: error: ‘_gruB5_rnnrf_flipflop_r941native5mC_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:214: error: ‘_gruB5_rnnrf_flipflop_r941native5mC_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:215: error: ‘_gruB5_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:217: error: ‘_FF_rnnrf_flipflop_r941native5mC_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:218: error: ‘_FF_rnnrf_flipflop_r941native5mC_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:224: error: ‘_conv_rnnrf_flipflop_r10Cpcr_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:225: error: ‘_conv_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:226: error: ‘conv_rnnrf_flipflop_r10Cpcr_stride’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:229: error: ‘_gruB1_rnnrf_flipflop_r10Cpcr_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:230: error: ‘_gruB1_rnnrf_flipflop_r10Cpcr_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:231: error: ‘_gruB1_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:233: error: ‘_gruF2_rnnrf_flipflop_r10Cpcr_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:234: error: ‘_gruF2_rnnrf_flipflop_r10Cpcr_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:235: error: ‘_gruF2_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:237: error: ‘_gruB3_rnnrf_flipflop_r10Cpcr_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:238: error: ‘_gruB3_rnnrf_flipflop_r10Cpcr_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:239: error: ‘_gruB3_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:241: error: ‘_gruF4_rnnrf_flipflop_r10Cpcr_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:242: error: ‘_gruF4_rnnrf_flipflop_r10Cpcr_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:243: error: ‘_gruF4_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:245: error: ‘_gruB5_rnnrf_flipflop_r10Cpcr_iW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:246: error: ‘_gruB5_rnnrf_flipflop_r10Cpcr_sW’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:247: error: ‘_gruB5_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:249: error: ‘_FF_rnnrf_flipflop_r10Cpcr_W’ undeclared here (not in a function) /projects/li-lab/software/flappie/src/networks.c:250: error: ‘_FF_rnnrf_flipflop_r10Cpcr_b’ undeclared here (not in a function) make[3]: *** [CMakeFiles/flappie_objects.dir/src/networks.c.o] Error 1 make[3]: Leaving directory /projects/li-lab/software/flappie/build'
make[2]: *** [CMakeFiles/flappie_objects.dir/all] Error 2
make[2]: Leaving directory /projects/li-lab/software/flappie/build' make[1]: *** [all] Error 2 make[1]: Leaving directory /projects/li-lab/software/flappie/build'
make: *** [build/flappie] Error 2
Truncated Q scores
I believe this is related to the previous issues. I am seeing some long reads which have truncated Q scores. I will send an example read by email.
Matt
/usr/bin/ld: cannot find -lblas
After I cloned the repository and run make:
-bash-4.1$ git clone https://github.com/nanoporetech/flappie
I have this issue:
[ 84%] Linking C executable flappie /usr/bin/ld: cannot find -lblas collect2: ld returned 1 exit status make[4]: *** [flappie] Error 1 make[4]: Leaving directory source/flappie/build'
make[3]: *** [CMakeFiles/flappie.dir/all] Error 2
make[3]: Leaving directory`
Any idea?
Thanks
Support RHEL and provide rpm packages
Would be great to get rpm packages and a repo for RHEL7 so we can just use "yum install flappie".
regards,
Hjalti Sveinsson
right model for Flappie & Guppy documentation
Hello,
It is the first time I am doing the basecalling on raw ONT data and I would like to run Flappie on the fast5 data.
I have a few questions:
The data (WGS on native plant DNA) was produced in October 2018 on a Promethion, basecalled one first time with guppy 1.6 (by the sequencing facility): I wonder if by using Flappie (on a cluster I have 1.1.0-73d731a) I will get a significant improvement on the quality of the base calls (attached is the report: there are many reads with quality below 7 and I would like to improve that).
Regarding the model, I see that r941_5mC outputs methylated bases as "Z" and it seems to be the only one available:
$ flappie --model help
r941_native : R9.4.1 model for MinION. Trained from native DNA library (default)
r941_5mC : R9.4.1 model for PromethION; 5mC aware. Trained from native NA12878 library
r10c_pcr : R10C model for MinION. Trained from PCR'd DNA library
or is it OK to use one for MinION?
What would be an expected output file size (including intermediate files) be for a e.g. 200 kb fast5?
The sys admin of the cluster informed me that the parallel option is not working. Is it better to run each folder containing the fast5 on a separate job? It looks like in Flappie I can’t specify threads. How much memory (approx) will I need for each job?
Would it be possible to select to keep only reads above QV7? Or should I do it outside? Which tool would you suggest?
Though Flappie seems to work (except for the Z bases), the alternative I have is Guppy (Version 2.3.1+1b9405b): is there a place where I can find good documentation on how to use it from command line?
Thanks,
Dario
how to deal with the signal to prepare for flowing into neural network
hi:
I am reading the codes, but I am confused how you deal with the raw signal to flow into neural network. Did you split the signals of each read by a constant windows length, and if so, did neighboring windows signal have overlap? Thank you.
Can't find cblas while trying to install dependencies via Conda
Hi there,
I'm trying to install Flappie on an environment without root, using Conda to install the dependencies. When I try to compile Flappie, it throws the error that it can't find cblas.h. This file is present in the Conda environment's /include directory.
(ont_sv) [koneill@hugin flappie]$ make flappie
cd build && \
cmake .. -DCMAKE_BUILD_TYPE=Release && \
make
-- Configuring done
-- Generating done
-- Build files have been written to: /projects/koneill_prj/Apps/flappie/build
make[1]: Entering directory `/projects/koneill_prj/Apps/flappie/build'
make[2]: Entering directory `/projects/koneill_prj/Apps/flappie/build'
make[3]: Entering directory `/projects/koneill_prj/Apps/flappie/build'
make[3]: Leaving directory `/projects/koneill_prj/Apps/flappie/build'
make[3]: Entering directory `/projects/koneill_prj/Apps/flappie/build'
[ 5%] Building C object CMakeFiles/flappie_objects.dir/src/layers.c.o
/projects/koneill_prj/Apps/flappie/src/layers.c:12:23: error: cblas.h: No such file or directory
Here are the contents of the Conda environment:
name: ont_sv
dependencies:
- canu=1.8
- sambamba=0.6.8
- bandage=0.8.1
- ngmlr=0.2.7
- sniffles=1.0.10
- nanosv=1.2.2
- git-lfs=2.6.1
- git=2.19.2
- cunit=2.1.3
- blas=1.1
- openblas=0.3.3
- libopenblas=0.3.3
- hdf5=1.10.4
- parallel=20181022
Multi-read fast5 support
Multi-read support for Flappie will come eventually but, since it is a research tool rather than a product, this isn’t a priority. Features proto-typed in Flappie will eventually be released into Guppy, which is our production basecaller, and this does support multi-read fast5.
There is a script available in the ont_fast5_api package (conversion_tools/multi_to_single_fast5.py) to convert a multi-read file into the old-style single-read files that are supported.
installation errors
Hi developers,
Thanks for the tool, there is some difficult in installation. I installed all the dependence flappie needed but still failed to install. Hope anyone could help me about that.
what training data used to train the model
Hi:
In the project , you train the 5mC model use NA12878 data. and then what data (species) you used to train the r94native model? Whether different species have a great influence as a training dataset? do you have some suggestion about choosing training dataset. Thank you very much.
guppy r941_5mC model ready?
Flappie can be used with the guppy r941_5mC model and produces good results although requires high compute. Is the guppy r941_5mC model ready? I couldn't find '5mC guppy' search hits in the community website.
Compilation errors:Makefile:34: recipe for target 'build/flappie' failed
Hi flappie community,
I'm getting compilation errors when compiling on ubuntu 16.04 servers with errors. Here is the compiler output:
cd build &&
cmake .. -DCMAKE_BUILD_TYPE=Release -DHDF5_ROOT='' &&
make flappie
/bin/sh: 2: cmake: not found
Makefile:34: recipe for target 'build/flappie' failed
make: *** [build/flappie] Error 127
error while making it can someone help me
hy when i do a make command this shows up:
gcc -O3 -flto -funsigned-char -falign-functions=16 -falign-loops=16 -falign-jumps=16 -Wall -Wextra -Wno-pointer-sign -Wno-sign-compare -pedantic -std=gnu99 brainflayer.o hex.o bloom.o mmapf.o hsearchf.o ec_pubkey_fast.o ripemd160_256.o dldummy.o algo/brainwalletio.o algo/warpwallet.o algo/keccak.o algo/sha3.o algo/brainv2.o secp256k1/.libs/libsecp256k1.a scrypt-jane/scrypt-jane.o -lrt -lcrypto -lz -lgmp -o brainflayer
/usr/bin/ld: /tmp/brainflayer.wvUox1.ltrans0.ltrans.o: in function main': <artificial>:(.text.startup+0x21f5): undefined reference to bloom_chk_hash160'
collect2: error: ld returned 1 exit status
make: *** [Makefile:68: brainflayer] Error 1
i have tried a few things but im allready out of ideas
thank you for your help
qname length
1 QNAME String [!-?A-~]{1,254}
Worth noting the above specification for qname lengths in sam/bam format. The current default for flappie is to use the filename as the query name and this breaks downstream tools if it is longer than sam/bam is expecting.
Matt
running flappie on ubuntu 16.04(run misc/trace_flipflop.py error)
Hi
I'm getting this error while checking trace viewer.why can i do?
Error message:
Traceback (most recent call last):
File "misc/trace_flipflop.py", line 187, in
'BaseCalled_template', 'Trace')][()]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/root/anaconda2/envs/py36/lib/python3.6/site-packages/h5py/_hl/group.py", line 262, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'Trace' doesn't exist)"
Thank
Compilation errors: layers.c collect2: ld returned 1 exit; "undefined reference to `cblas_sgemv'"
Hi flappie community,
I'm getting compilation errors when compiling on CentOS6.8 servers with errors referring to cblas_*. Here is the compiler output:
[rahmed@cel flappie]$ make flappie
cd build && \
cmake .. -DCMAKE_BUILD_TYPE=Release && \
make
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rahmed/cunit/flappie/build
make[1]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[2]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[3]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[3]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
[ 39%] Built target flappie_objects
make[3]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[3]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
[ 43%] Built target flappie_static
make[3]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[3]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[3]: Entering directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
[ 47%] Linking C executable flappie
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `set_compression':
fast5_interface.c:(.text+0x34e): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_trace':
fast5_interface.c:(.text+0xfc5): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
CMakeFiles/flappie.dir/src/fast5_interface.c.o: In function `write_signal':
fast5_interface.c:(.text+0x113e): undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
libflappie.a(layers.c.o): In function `lstm_step':
layers.c:(.text+0x21c): undefined reference to `cblas_sgemv'
libflappie.a(layers.c.o): In function `gru_step':
layers.c:(.text+0x7c4): undefined reference to `cblas_sgemv'
layers.c:(.text+0x98f): undefined reference to `cblas_sgemv'
layers.c:(.text+0xb61): undefined reference to `cblas_sgemv'
libflappie.a(layers.c.o): In function `grumod_step':
layers.c:(.text+0xdda): undefined reference to `cblas_sgemv'
libflappie.a(layers.c.o):layers.c:(.text+0x2294): more undefined references to `cblas_sgemv' follow
libflappie.a(layers.c.o): In function `convolution':
layers.c:(.text+0x3010): undefined reference to `cblas_sgemm'
layers.c:(.text+0x3172): undefined reference to `cblas_sgemv'
libflappie.a(flappie_matrix.c.o): In function `affine_map2':
flappie_matrix.c:(.text+0x169a): undefined reference to `cblas_sgemm'
flappie_matrix.c:(.text+0x16fa): undefined reference to `cblas_sgemm'
libflappie.a(flappie_matrix.c.o): In function `affine_map':
flappie_matrix.c:(.text+0x1833): undefined reference to `cblas_sgemm'
collect2: ld returned 1 exit status
make[3]: *** [flappie] Error 1
make[3]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[2]: *** [CMakeFiles/flappie.dir/all] Error 2
make[2]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/pbtech_mounts/homes024/rahmed/cunit/flappie/build'
make: *** [build/flappie] Error 2
flappie was cloned with git-lfs with cblas.h present in system library locations as well as openblas, openblas-devel for good measure.
The versions of the dependencies used are:
cmake: 3.11.2
cunit: 2.1.3
hdf5: 1.10.2
openblas: 0.2.20
openmpi was loaded after previous errors and that resolved a previous error that is now good. I also tried compiling with glibc2.14 as some lines in the "LD_DEBUG=all make flappie" error log looked like that might have been the culprit. That didn't help either.
Here is the "LD_DEBUG=all make flappie" cmake log. It's quite large.
The "undefined reference" errors lead me to suspect that there may be some missing files that weren't downloaded. Any help is appreciated.
Thanks,
Rashad
best accuracies for direct RNA
Do you have any direct comparison metrics for various options to basecall direct RNA runs
-
guppy with production models v.3.3.0 onwards (I think this was the last time RNA model was updated for accuracy). How stable have these models been.
-
flappie with the version 2 flipflop model, did this one make its way into guppy production? Was from March this year
flipflop5_202003_r941rna002_ff2161d3.mdl -
Rerio research model released direct RNA model
res_rna2_r941_min_flipflop_v001.cfg
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Google ❤️ Open Source for everyone.
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Alibaba
Alibaba Open Source for everyone
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D3
Data-Driven Documents codes.
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Tencent
China tencent open source team.