Error in installing DeepRepeat

[Cesco16]

Hi there,

I would like to use try this interesting software. I tried to install it using anaconda. I followed the instructions on the github page but, after typing

h5c++ -03 -std=c++11 [...]

I got the following error:

BamReader.c: In member function ‘int BamReadOption::set_w_qry_seq(bool)’: BamReader.c:136:72: warning: no return statement in function returning non-void [-Wreturn-type] int BamReadOption::set_w_qry_seq(bool mqryseq){ m_w_qry_seq = mqryseq; } ^ BamReader.c: In member function ‘int BamReadOption::set_w_map_detail(bool, bool, char, int)’: BamReader.c:143:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ BamReader.c: In member function ‘int BamReadOption::set_w_qry_qual(bool)’: BamReader.c:145:74: warning: no return statement in function returning non-void [-Wreturn-type] int BamReadOption::set_w_qry_qual(bool mqryqual){ m_w_qry_qual=mqryqual; } ^ In file included from Fast5Reader.c:1: Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Channel()’: Fast5Reader.h:133:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Channel(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Fastq()’: Fast5Reader.h:134:31: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Fastq(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Events()’: Fast5Reader.h:135:32: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Events(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Signals()’: Fast5Reader.h:136:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Signals(){;} ^ Fast5Reader.c: In member function ‘int F5Reader::init(const char, RunOption)’: Fast5Reader.c:219:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ Fast5Reader.c: In member function ‘int F5Reader::del()’: Fast5Reader.c:224:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ Fast5Reader.c: In member function ‘int F5Reader::resetFast5File(const char, RunOption)’: Fast5Reader.c:247:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ Fast5Reader.c: In member function ‘int F5Reader::normalize_signal()’: Fast5Reader.c:893:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from RepeatFeatExtract.h:7, from RepeatFeatExtract.c:5: Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Channel()’: Fast5Reader.h:133:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Channel(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Fastq()’: Fast5Reader.h:134:31: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Fastq(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Events()’: Fast5Reader.h:135:32: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Events(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Signals()’: Fast5Reader.h:136:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Signals(){;} ^ In file included from RepeatFeatExtract.h:7, from genomic1FE.c:14: Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Channel()’: Fast5Reader.h:133:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Channel(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Fastq()’: Fast5Reader.h:134:31: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Fastq(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Events()’: Fast5Reader.h:135:32: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Events(){;} ^ Fast5Reader.h: In member function ‘virtual int F5Reader::readF5Signals()’: Fast5Reader.h:136:33: warning: no return statement in function returning non-void [-Wreturn-type] virtual int readF5Signals(){;} ^ /usr/bin/ld: Fast5Reader.o: in function `F5Reader::init(char const, RunOption*)': Fast5Reader.c:(.text+0x16e7): undefined reference to H5::H5File::H5File(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, H5::FileCreatPropList const&, H5::FileAccPropList const&)' /usr/bin/ld: Fast5Reader.o: in functionF5Reader::readF5Channel(std::cxx11::basic_string<char, std::char_traits, std::allocator >)': Fast5Reader.c:(.text+0x3f34): undefined reference to `H5::H5Location::openGroup(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x3fb0): undefined reference to H5::H5Object::openAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x405d): undefined reference toH5::H5Object::openAttribute(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x413b): undefined reference to `H5::H5Object::openAttribute(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x421c): undefined reference to H5::H5Object::openAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /usr/bin/ld: Fast5Reader.o: in functionF5Reader::readF5Fastq(std::cxx11::basic_string<char, std::char_traits, std::allocator >)': Fast5Reader.c:(.text+0x49d5): undefined reference to `H5::H5Location::openDataSet(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x4b06): undefined reference to H5::DataSet::read(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, H5::DataType const&, H5::DataSpace const&, H5::DataSpace const&, H5::DSetMemXferPropList const&) const' /usr/bin/ld: Fast5Reader.o: in functionF5Reader::readF5Events(std::cxx11::basic_string<char, std::char_traits, std::allocator >)': Fast5Reader.c:(.text+0x5f0f): undefined reference to `H5::H5Location::openDataSet(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x60b1): undefined reference to H5::CompType::insertMember(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, H5::DataType const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x6145): undefined reference toH5::CompType::insertMember(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned long, H5::DataType const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x61d9): undefined reference to `H5::CompType::insertMember(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned long, H5::DataType const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x626d): undefined reference to H5::CompType::insertMember(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, H5::DataType const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x6326): undefined reference toH5::CompType::insertMember(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned long, H5::DataType const&) const' /usr/bin/ld: Fast5Reader.o:Fast5Reader.c:(.text+0x63c5): more undefined references to `H5::CompType::insertMember(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned long, H5::DataType const&) const' follow /usr/bin/ld: Fast5Reader.o: in function F5Reader::_readF5Signals_(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)': Fast5Reader.c:(.text+0x6b7c): undefined reference toH5::H5Location::openDataSet(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x6bb1): undefined reference to `H5::DataSet::read(std::cxx11::basic_string<char, std::char_traits, std::allocator >&, H5::DataType const&, H5::DataSpace const&, H5::DataSpace const&, H5::DSetMemXferPropList const&) const' /usr/bin/ld: Fast5Reader.o: in function F5Reader1::readF5Signals()': Fast5Reader.c:(.text+0x70f8): undefined reference toH5::H5Location::openGroup(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' /usr/bin/ld: Fast5Reader.c:(.text+0x71e6): undefined reference to `H5::H5Location::getObjnameByIdx[abi:cxx11](unsigned long long) const' collect2: error: ld returned 1 exit status

Any tips on how to fix it? Thank you very much!

[liuqianhn]

@Cesco16 , Thank you for being interested in the tools. Here are my suggestions:

1. You can try the docker docker run --rm genomicslab/deeprepeat:0.1.3 where you do not need to compile DeepRepeat.
2. The issues are from 2 sources: one is compiling option----please remove something like -W*error* from the compiling command; the other is the installation issue of hdf5. Please show the whole compiling command for investigating the detail (need compiling options or installation issue of hdf5?)

[Cesco16]

Hi, thank you! I would like to solve the problem without using docker (if possible). This is the whole command:

h5c++ -O3 -std=c++11 -I $DR_conda_base/include -L$DR_conda_base/lib -lhts -o genomic1FE ComFunction.c ComOption.c BamReader.c Fast5Index.c Fast5Reader.c RepeatFeatExtract.c genomic1FE.c $DR_conda_base//lib/libhdf5_hl_cpp.a $DR_conda_base//lib/libhdf5_cpp.a $DR_conda_base//lib/libhdf5_hl.a $DR_conda_base//lib/libhdf5.a -lz -ldl -lpthread

I just followed the installation instructions on github. Thank you very much!

[Cesco16]

I tried to repeat the instructions in the github page. Now, I created the conda environment using the environment.yml file provided. Now, I got a different error message:

condapath/envs/py36deeprepeat/bin/h5c++: 1: eval: condapath/envs/py36deeprepeat/bin/x86_64-conda_cos6-linux-gnu-c++: not found

In fact, if I go to py36deeprepeat folder I found :

x86_64-conda_cos7-linux-gnu-c++

How to solve this? Maybe it is more simple than previous issue. Thanks

[liuqianhn]

@Cesco16 It seems that it is the installation issue of gxx_linux-64. please try to reinstall "conda install gxx_linux-64".

[Cesco16]

Hi, unfortunately, it did not work. Which version of anaconda or miniconda do you use to run DeepRepeat?

[liuqianhn]

@Cesco16 I tested anaconda3 with python 3.6 on Ubuntu 20.04.4 LTS and CentOS 6 (not sure, @umahsn could you please help to check OS version on CHOP cluster?).

[umahsn]

Currently CHOP cluster is running "Red Hat Enterprise Linux 8.5 (Ootpa)", and I think it has been the OS for at least a year now.

[liuqianhn]

@umahsn Thank you very much. DeepRepeat was developed more than 1 year ago and CHOP cluster has the older OS(I remember the old OS is centos 6 or 7, but forgot which one).

[Cesco16]

Hi, I tried to install it using a miniconda version of few years ago. It gave me some warnings but no errors during compiling operations. When I tried it to a sample, it gives me the following errors:

python DeepRepeat/bin/DeepRepeat.py Detect --bam Repeats/my_file.bam --o Repeats/ --repeat "chr19:45770061-45770481:TGC:3" --f5folder Repeats/fast5_pass

/path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:523: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:524: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:527: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /path/miniconda3/envs/py36deeprepeat2/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:532: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) The following options are used (included default): UniqueID (mpred); bam (Repeats/my_file.bam); basecalled_path (workspace/pass/); f5config (/path/DeepRepeat/bin/data/config/fast5_path.config); f5folder (Repeats/fast5_pass); f5i (Repeats/fast5_pass/f5.f5index); f5i_basefile (f5); feature_num (50); label_size (4); merge_gap (4.5); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (Repeats/); pcr (False); repeat (chr19:45770061-45770481:TGC:3); repeat_name (m_repeat); repeat_pat (TGC); rpg (/path/DeepRepeat/bin/data/trf.v0.bed); summary_file (Repeats/fast5_pass/sequencing_summary.txt);

Generating f5index: /path/DeepRepeat/bin/scripts/IndexF5files Repeats/fast5_pass workspace/pass/ f5 Repeats/fast5_pass/sequencing_summary.txt 0 Options to be used: base_index_path = Repeats/fast5_pass basecalled_path = workspace/pass/ uniq_id = f5 seq_sum = Repeats/fast5_pass/sequencing_summary.txt multifast5 = 0

The input sequencing summary are: Repeats/fast5_pass/sequencing_summary.txt The basecall path is <workspace/pass/> The output index file is <Repeats/fast5_pass/f5.f5index> <Repeats/fast5_pass/workspace/pass//.fast5> has 0 fast5 files

Base index is saved in <Repeats/fast5_pass/f5.f5index>. Please keep this file together with its indexed fast5 folders. You might need to provide this file for feature extraction and repeat detection. Generating features: /path/DeepRepeat/bin/scripts/genomic1FE Repeats/my_file.bam Repeats//mpred.fs Repeats/fast5_pass/ Repeats/fast5_pass/f5.f5index chr19:45770061-45770481:TGC:3 /path/DeepRepeat/bin/data/trf.v0.bed /path/DeepRepeat/bin/data/config/fast5_path.config -1.5 100 p_f5_conf_file /path/DeepRepeat/bin/data/config/fast5_path.config Input = Repeats/my_file.bam Repeats//mpred.fs free(): invalid size Aborted Error! Cannot generate fs file: Repeats//mpred.fs

I did not understand

[liuqianhn]

Hi @Cesco16 The warning will not cause the error. The issue is that <Repeats/fast5_pass/workspace/pass//.fast5> has 0 fast5 files: it seems that no fast5 are found.

1. What is in the folder of Repeats/fast5_pass
2. Are you able to run a simple example from https://github.com/WGLab/DeepRepeat/blob/master/docs/Reproducibility.md

[Cesco16]

Hi @liuqianhn In folder Repeats/fast5_pass I have 484 .fast5 files (obtained from MinION MK1C) and the sequencing_summary.txt file. Ok, I can try to run an example and I will keep you updated. Thank you!

[liuqianhn]

@Cesco16 Thank you for your update. It will be better you can share the folder structure under Repeats/fast5_pass, by default, it assumes that there is a subfolder workspace/pass/ under the basefold for fast5 files.

[Cesco16]

Hi @liuqianhn ,

Ok, I will try also to put the subfolder workspace/pass/

Anyway, I tried to run an example of the ones provided. I downloaded the well-trained model and I created the folder structure shown in the github page. I run the following command:

python DeepRepeat/bin/DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o test_op/AGAT_chr6_145272942-145273029 --bam na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500 2>&1 | grep "GMM:"

It seems it was successful. But the output folder test_op/AGAT_chr6_145272942-145273029 is empty. What could be the error?

[liuqianhn]

please run python DeepRepeat/bin/DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o test_op/AGAT_chr6_145272942-145273029 --bam na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500, and you will see output from stdout.

[Cesco16]

Hi @liuqianhn , done, this is the result (error):

The following options are used (included default): UniqueID (AGAT_chr6_145272942-145273029); bam (na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam); basecalled_path (workspace/pass/); f5config (/path/DeepRepeat/bin/data/config/fast5_path.config); f5folder (na12878_loci/AGAT_chr6_145272942-145273029); f5i (na12878_loci/AGAT_chr6_145272942-145273029/na.f5index); f5i_basefile (na); feature_num (50); label_size (4); merge_gap (6.0); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (test_op/AGAT_chr6_145272942-145273029); pcr (True); repeat (chr6:145272942-145273029:AGAT:4); repeat_name (AGAT_chr6_145272942-145273029); repeat_pat (AGAT); rpg (/path/DeepRepeat/bin/data/trf.v0.bed); summary_file (na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Generating features: path/DeepRepeat/bin/scripts/genomic1FE na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs na12878_loci/AGAT_chr6_145272942-145273029/ na12878_loci/AGAT_chr6_145272942-145273029/na.f5index chr6:145272942-145273029:AGAT:4 path/DeepRepeat/bin/data/trf.v0.bed path/DeepRepeat/bin/data/config/fast5_path.config -1.5 500 p_f5_conf_file path/DeepRepeat/bin/data/config/fast5_path.config Input = na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs free(): invalid size Aborted Error! Cannot generate fs file: test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs

[liuqianhn]

I guess it is the issue others have. Please try to install glibc-source (please note that: does NOT install glibc especially with root permission, since the installation of glibc will crash your OS).

[Cesco16]

Hi @liuqianhn , thank you for the suggestion! How to install it in a proper way?

[liuqianhn]

@Cesco16 You need to talk to your manager who has root permission of the computers you are working on. Make sure to install correct glibc-source rather than glibc. Some command in Ubuntu is sudo apt-get install glibc-source

[Cesco16]

Hi @liuqianhn , I am trying to run DeepRepeat using Docker because of problems for root permission for the anaconda method. I am trying to run the example. Is it possible that the sequencing_summary.txt file is not present in the na12878_loci folder to download to run the example? How to deal with? Thank you

[liuqianhn]

@Cesco16 For each loci subfolder, there should be na.f5index. If this file exist, you do not need sequencing_summary.txt file

[Cesco16]

Hi @liuqianhn , this is the error message:

Error happen! na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt does not exist. Should specified by --summary_file.

I used the command you provided me some days ago, without using the --summary_file option

[Cesco16]

I forgot to specify that this error happens even if the na.f5index file does exist and is in the loci subfolder.

[Cesco16]

Hi @liuqianhn,
I copy and paste here the whole command:

docker run --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o test_op/AGAT_chr6_145272942-145273029 --bam na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500 The following options are used (included default): UniqueID (AGAT_chr6_145272942-145273029); bam (na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam); basecalled_path (workspace/pass/); f5config (data/config/fast5_path.config); f5folder (na12878_loci/AGAT_chr6_145272942-145273029); f5i (na12878_loci/AGAT_chr6_145272942-145273029/na.f5index); f5i_basefile (na); feature_num (50); label_size (4); merge_gap (6.0); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (test_op/AGAT_chr6_145272942-145273029); pcr (True); repeat (chr6:145272942-145273029:AGAT:4); repeat_name (AGAT_chr6_145272942-145273029); repeat_pat (AGAT); rpg (data/trf.v0.bed); summary_file (na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Error happen! na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt does not exist. Should specified by --summary_file.

I hope it can help in finding a solution Thank you!

[liuqianhn]

@Cesco16 When running docker, you need to map your current folder to the docker folder. Please check the commands below (after replace CURRENT_FOLDER with your current running folder)

docker run -v "CURRENT_FOLDER":/project/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /project/test_op/AGAT_chr6_145272942-145273029 --bam /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /project/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

[Cesco16]

Hi @liuqianhn , how to get the docker folder? I found a path that is: /C/ProgramData/DockerDesktop/ and I substituted it to /project/. I also moved the folders (na12878_loci, test_op, trainedmod, etc..) to that path. However, when running the command you gave me, I got the same error as before:

docker run -v C/Users/Lenovo/:/C/ProgramData/DockerDesktop/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o C/ProgramData/DockerDesktop/test_op/AGAT_chr6_145272942-145273029 --bam C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500 The following options are used (included default): UniqueID (AGAT_chr6_145272942-145273029); bam (C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam); basecalled_path (workspace/pass/); f5config (data/config/fast5_path.config); f5folder (C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029); f5i (C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index); f5i_basefile (na); feature_num (50); label_size (4); merge_gap (6.0); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (C/ProgramData/DockerDesktop/test_op/AGAT_chr6_145272942-145273029); pcr (True); repeat (chr6:145272942-145273029:AGAT:4); repeat_name (AGAT_chr6_145272942-145273029); repeat_pat (AGAT); rpg (data/trf.v0.bed); summary_file (C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Error happen! C/ProgramData/DockerDesktop/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt does not exist. Should specified by --summary_file.

Sorry, but I am pretty new in using docker by terminal

[liuqianhn]

@Cesco16 please use your current folder to replace "CURRENT_FOLDER", and keep /project/ unchanged. For example, if the folder you have for na12878_loci is "/C/PD/D/na12878_loci", replace "CURRENT_FOLDER" by "/C/PD/D/"

[Cesco16]

If I understood well, this is what I should type in terminal:

/C/U/L/Desktop$ docker run -v /C/U/L/Desktop/:/project/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /C/U/L/Desktop/test_op/AGAT_chr6_145272942-145273029 --bam /C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

But it gave me same error again:

The following options are used (included default): UniqueID (AGAT_chr6_145272942-145273029); bam (/C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam); basecalled_path (workspace/pass/); f5config (data/config/fast5_path.config); f5folder (/C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029); f5i (/C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index); f5i_basefile (na); feature_num (50); label_size (4); merge_gap (6.0); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (/C/U/L/Desktop/test_op/AGAT_chr6_145272942-145273029); pcr (True); repeat (chr6:145272942-145273029:AGAT:4); repeat_name (AGAT_chr6_145272942-145273029); repeat_pat (AGAT); rpg (data/trf.v0.bed); summary_file (/C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Error happen! /C/U/L/Desktop/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt does not exist. Should specified by --summary_file.

Sorry for disturbing again!

[liuqianhn]

@Cesco16 Do you have na12878_loci/AGAT_chr6_145272942-145273029/na.f5index? If this file exists, --summary_file is not necessary.

[Cesco16]

Hi @liuqianhn , Yes, I have it

[liuqianhn]

@Cesco16 In your setting, your command should be

/C/U/L/Desktop$ docker run -v /C/U/L/Desktop/:/project/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /project/test_op/AGAT_chr6_145272942-145273029 --bam /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /project/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

Please do NOT replace /project/, and make sure that you have /C/U/L/Desktop/na12878_loci/.

[Cesco16]

Hi @liuqianhn , this is the error it gives me after typing the command above:

docker: Error response from daemon: invalid mode: /project/.

[liuqianhn]

@Cesco16 Please share the command you run. It seems that you include specific characters in, and /project/ is not a part of the parameter for -v

[Cesco16]

Hi @liuqianhn , this is the whole command I used:

C:/Users/Lenovo/Desktop> docker run -v /C:/Users/Lenovo/Desktop/:/project/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /project/test_op/AGAT_chr6_145272942-145273029 --bam /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /project/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

[Cesco16]

Hi @liuqianhn , can you please write all the needed steps to correctly download and use docker version of DeepRepeat? Maybe I could have missed some steps that cause the error. I don't know. Thank you!

[Cesco16]

Hi @liuqianhn , I tried to change the command, and now it seems it does work, even if a differen error rised:

docker run -v //c/Users/Lenovo/Desktop/://project/ --rm genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /project/test_op/AGAT_chr6_145272942-145273029 --bam /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /project/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500 The following options are used (included default): UniqueID (AGAT_chr6_145272942-145273029); bam (/project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam); basecalled_path (workspace/pass/); f5config (data/config/fast5_path.config); f5folder (/project/na12878_loci/AGAT_chr6_145272942-145273029); f5i (/project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index); f5i_basefile (na); feature_num (50); label_size (4); merge_gap (6.0); mod_path (None); mod_version (2); multif5 (0); nb_size (3); nbsize (-1.5); outlog (0); outputfolder (/project/test_op/AGAT_chr6_145272942-145273029); pcr (True); repeat (chr6:145272942-145273029:AGAT:4); repeat_name (AGAT_chr6_145272942-145273029); repeat_pat (AGAT); rpg (data/trf.v0.bed); summary_file (/project/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Generating features: /app/scripts/genomic1FE /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs /project/na12878_loci/AGAT_chr6_145272942-145273029/ /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index chr6:145272942-145273029:AGAT:4 data/trf.v0.bed data/config/fast5_path.config -1.5 500 free(): invalid size p_f5_conf_file data/config/fast5_path.config Input = /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs Aborted Error! Cannot generate fs file: /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs

How to deal with?

[liuqianhn]

@umahsn @kaichop Could you please ask someone to test it in biocluster? During the test step, please write down the commands step-by-step and share it. It seems that it is an issue of missing some system packages, but do not know which one. Thanks.

[Cesco16]

Hi @liuqianhn, are there any news from your side?

[liuqianhn]

@umahsn @kaichop Any test to be shared?

[umahsn]

@liuqianhn I also got the same error.

Here is what I tested:

wget https://github.com/WGLab/DeepRepeat/releases/download/v0.1.3/na12878_loci_nanopore.tar.gz
tar -xvf na12878_loci_nanopore.tar.gz

docker run -v $PWD:"/project/" genomicslab/deeprepeat:0.1.4 python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /project/test_op/AGAT_chr6_145272942-145273029 --bam /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /project/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

And this is the error I got:

The following options are used (included default):
            UniqueID    (AGAT_chr6_145272942-145273029);
                 bam    (/project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam);
     basecalled_path    (workspace/pass/);
            f5config    (data/config/fast5_path.config);
            f5folder    (/project/na12878_loci/AGAT_chr6_145272942-145273029);
                 f5i    (/project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index);
        f5i_basefile    (na);
         feature_num    (50);
          label_size    (4);
           merge_gap    (6.0);
            mod_path    (None);
         mod_version    (2);
             multif5    (0);
             nb_size    (3);
              nbsize    (-1.5);
              outlog    (0);
        outputfolder    (/project/test_op/AGAT_chr6_145272942-145273029);
                 pcr    (True);
              repeat    (chr6:145272942-145273029:AGAT:4);
         repeat_name    (AGAT_chr6_145272942-145273029);
          repeat_pat    (AGAT);
                 rpg    (data/trf.v0.bed);
        summary_file    (/project/na12878_loci/AGAT_chr6_145272942-145273029/sequencing_summary.txt);

Generating features: /app/scripts/genomic1FE  /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs /project/na12878_loci/AGAT_chr6_145272942-145273029/ /project/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index chr6:145272942-145273029:AGAT:4 data/trf.v0.bed data/config/fast5_path.config -1.5 500
p_f5_conf_file data/config/fast5_path.config
Input = /project/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs
free(): invalid size
Aborted (core dumped)
Error! Cannot generate fs file: /project/test_op/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.fs

[umahsn]

I tried to repeat the instructions in the github page. Now, I created the conda environment using the environment.yml file provided. Now, I got a different error message:

condapath/envs/py36deeprepeat/bin/h5c++: 1: eval: condapath/envs/py36deeprepeat/bin/x86_64-conda_cos6-linux-gnu-c++: not found

In fact, if I go to py36deeprepeat folder I found :

x86_64-conda_cos7-linux-gnu-c++

How to solve this? Maybe it is more simple than previous issue. Thanks

This can be fixed by changing the environment.yml to specify gcc version as follows: gxx_linux-64=9.3

I will changed that in the .yml file. Perhaps recompiling with all compiler warnings enabled will give better look into what is causing the error in freeing the null pointer.

[pmitev]

I did fix it (not so nicely done but...) by using the precompiled binaries in the repository and export LD_LIBRARY_PATH=${DR_conda_base}/lib and it works in both the conda environment setup and in a Singularity container. Here is the Singularity recipe that works for me https://github.com/pmitev/UPPMAX-Singularity/blob/main/DeepRepeat/DeepRepeat.def

Seems that gxx_linux-64=7.5 in environment.yml solves the problem as well - here is an alternative build https://github.com/pmitev/UPPMAX-Singularity/blob/main/DeepRepeat/DeepRepeat-7.5.def

[Cesco16]

Hi @pmitev, do you mean the following:

git clone https://github.com/WGLab/DeepRepeat cd DeepRepeat conda env create -f environment.yml source activate py36deeprepeat #if you change conda env name, please replace py36deeprepeat cd bin/scripts export DR_conda_base="/home/xxx/anaconda2/envs/py36deeprepeat/" export LD_LIBRARY_PATH=${DR_conda_base}/lib g++ -O3 -std=c++11 -o IndexF5files ComFunction.c Fast5Index.c IndexF5files.c h5c++ -O3 -std=c++11 -I $DR_conda_base/include -L$DR_conda_base/lib -lhts -o genomic1FE ComFunction.c ComOption.c BamReader.c Fast5Index.c Fast5Reader.c RepeatFeatExtract.c genomic1FE.c $DR_conda_base//lib/libhdf5_hl_cpp.a $DR_conda_base//lib/libhdf5_cpp.a $DR_conda_base//lib/libhdf5_hl.a $DR_conda_base//lib/libhdf5.a -lz -ldl -lpthread

? And should it work?

[pmitev]

If you choose to go with export LD_LIBRARY_PATH=${DR_conda_base}/lib just skip the 2 compiling steps. They are precompiled in the repository some 17 months ago...

Or if you want to compile, in the environment.yml change the last line from gxx_linux-64=9.3 to gxx_linux-64=7.5.

[Cesco16]

Ok! Now it seems to work! Thank you very much! I tried to run it on one of the examples provided (na12878_loci/AGAT_4 and I got two files in test_op folder:

AGAT_chr6_145272942-145273029.fs AGAT_chr6_145272942-145273029.fs.more

Is it right?

I opened the .fs file and I have the following (first 10 lines):

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273158 3 1 0 0 0 16 1.60227 0.142422 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 63 143 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273157 3 1 0 0 0 10 0.734545 0.37511 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 25 25 51 25 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273156 3 1 0 0 0 4 -0.877273 0.464327 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 63 63 0 0 0 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273154 3 1 0 0 0 3 0.484848 0.636162 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 0 0 0 85 0 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273153 3 1 0 0 0 9 -0.945455 0.493707 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 56 56 85 0 0 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273152 3 1 0 0 0 5 1.77091 0.234707 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 0 102 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273151 3 1 0 0 0 2 0.690909 0.0909091 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 255 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273150 3 1 0 0 0 3 0.248485 0.111423 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 170 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 145273149 3 1 0 0 0 8 0.215909 0.115149 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 127 95 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

How to correctly read the output? Thank you very much in advance!

[liuqianhn]

Hi All, sorry for the late reply.

@umahsn Thank you very much for your testing.

@pmitev Many thanks for the great solution. It did solve the problems.

@Cesco16 The output you shared in the .fs file is not the final output, but the input of the second step. The final output is in the stdout with a line starting with "GMM: "

[Cesco16]

Hi @liuqianhn , sorry for the inconvenient. I used the following command:

python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /mnt/c/users/lenovo/desktop/DeepRepeat/test_op/AGAT_chr6_145272942-145273029 --bam /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500

but I get this error:

OSError: File trainedmod_32_0.2/hx1/AGAT_4/200_v0.2motif32/np_dl_4.meta does not exist.

But this file is present!

[liuqianhn]

@Cesco16 since you do not specify --mod_path, the default path for the trained_mod is your running folder. Could you please share where is the *.meta files and where you run the command? Thanks.

[Cesco16]

@liuqianhn now I tried to specifiy the path using the command --mod_path

python DeepRepeat.py Detect --gn hx1 --TempRem 0 --epchon 200 --repeat_relax_bp 20 --UniqueID AGAT_chr6_145272942-145273029 --is_pcr 0 --repeatName AGAT_chr6_145272942-145273029 --repeat chr6:145272942-145273029:AGAT:4 --f5i /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029/na.f5index --o /mnt/c/users/lenovo/desktop/DeepRepeat/test_op/AGAT_chr6_145272942-145273029 --bam /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029/AGAT_chr6_145272942-145273029.bam --f5folder /mnt/c/users/lenovo/desktop/DeepRepeat/na12878_loci/AGAT_chr6_145272942-145273029 --algLen 500 --mod_path /mnt/c/users/lenovo/desktop/DeepRepeat/trainedmod_32_0.2/hx1/AGAT_4/200_v0.2motif32/np_dl_4

This is what I get:

Warning!!!! could not find optimized model

0 17.900m 5 0.490004665st 1 0.000m 1 0.000001000st 12 2 13.667m 4 0.222283755st 3 15.000m 7 0.000001000st keep 0 17.900m 5 0.490004665st 10 1 0.000m 1 0.000001000st 3 2 13.667m 4 0.222283755st 13 0 0 1 1 18 0 < False > True [18, 17.899998814258634, 5, 0.49000466492082595, 10] 18 10 1 1 12 18 < False > False [12, 0.0, 1, 1e-06, 3] 18 10 1 1 14 18 < False > True [14, 13.666718479195692, 4, 0.22228375490163696, 13] peak2 [14] {18: []} peak2 [14, 18] {18: []} peak2 [14, 18] peak2 [14, 18] GMM: AGAT_chr6_145272942-145273029-AGAT [14, 18] allocr:12:1, 13:2, 14:4, 15:7, 16:1, 17:3, 18:5, 19:2, 20:1, Testing Finished! True

[liuqianhn]

@Cesco16 It seems that the running is successful. The test suggests that the potential repeat counts are 14 and 18. The warning message is because it is hard to find optimized model for peak calling. For the output you have, I think the repeat counts of the two alleles are 15 and 18 based on the last third ling of the output you shared.