# Analysis says 100% unknown?

**URL:** <https://forum.biobakery.org/t/analysis-says-100-unknown/3681>\
**Category:** MetaPhlAn\
**Created:** [June 3, 2022, 5:44pm UTC](https://forum.biobakery.org/t/analysis-says-100-unknown/3681 "2022-06-03T17:44:57Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![sgetto](https://avatars.discourse-cdn.com/v4/letter/s/41988e/32.png) [@sgetto](https://forum.biobakery.org/u/sgetto)\
**Post date:** [June 3, 2022, 5:44pm UTC](https://forum.biobakery.org/t/analysis-says-100-unknown/3681/1 "2022-06-03T17:44:57Z")

</div>

Hi all,

I am trying to run metagenomic profiling on one read (the fwd one) from paired end shot gun sequencing. Everything seems to work- I ran a tutorial with the Supragingival\_plaque.fasta and it worked great. When I tried to use my own files I don’t get any error messages but I get this result:

 ![Screen Shot 2022-06-03 at 11.41.25 AM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/7/7beb1034b27b80281f4fb9b115bb2649afc689e0.png)

the bowtie output file looks like this:

 ![Screen Shot 2022-06-03 at 11.46.10 AM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/4/4fdd0638d5099927f9c6f6bf60bcd5d50d703a3e.png)

Here is the code I used for the run:

 ![Screen Shot 2022-06-03 at 11.41.48 AM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/5/5f557e392a2dde56e190d59d95a14389c515b9cc.png)

And if it helps, here’s all the code from downloading MetaPhlAn and its databases:  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels defaults  
Warning: ‘defaults’ already in ‘channels’ list, moving to the top  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels bioconda  
Warning: ‘bioconda’ already in ‘channels’ list, moving to the top  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda config --add channels conda-forge  
Warning: ‘conda-forge’ already in ‘channels’ list, moving to the top  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda create --name mpa -c bioconda python=3.7 metaphlan  
Collecting package metadata (current\_repodata.json): done  
Solving environment: done

==\> WARNING: A newer version of conda exists. \<==  
current version: 4.12.0  
latest version: 4.13.0

Please update conda by running

```
$ conda update -n base conda

```

## Package Plan

environment location: /Users/stephaniegetto/opt/anaconda3/envs/mpa

added / updated specs:  
- metaphlan  
- python=3.7

The following packages will be downloaded:

```
package | build
---------------------------|-----------------
biom-format-2.1.12 | py37h49e79e5_1 10.4 MB conda-forge
biopython-1.79 | py37h271585c_1 2.6 MB conda-forge
bowtie2-2.4.5 | py37h0f016ca_2 1.4 MB bioconda
brotlipy-0.7.0 |py37h69ee0a8_1004 366 KB conda-forge
bx-python-0.8.13 | py37h2b10027_1 931 KB bioconda
certifi-2022.5.18.1 | py37hf985489_0 150 KB conda-forge
cffi-1.15.0 | py37h446072c_0 218 KB conda-forge
click-8.1.3 | py37hf985489_0 145 KB conda-forge
cryptography-37.0.2 | py37h0169fcd_0 1.2 MB conda-forge
fonttools-4.33.3 | py37h994c40b_0 1.6 MB conda-forge
future-0.18.2 | py37hf985489_5 709 KB conda-forge
h5py-3.6.0 |nompi_py37h0ac0de7_100 1.1 MB conda-forge
importlib-metadata-4.11.4 | py37hf985489_0 33 KB conda-forge
kiwisolver-1.4.2 | py37h18621fa_1 61 KB conda-forge
matplotlib-base-3.5.2 | py37h80cb303_0 7.4 MB conda-forge
metaphlan-3.0.14 | pyhb7b1952_0 237 KB bioconda
numpy-1.21.6 | py37h345d48f_0 6.0 MB conda-forge
pandas-1.3.4 | py37h5b83a90_1 11.3 MB conda-forge
pillow-9.1.1 | py37h1eb1bbc_1 44.5 MB conda-forge
pysam-0.19.1 | py37h64e44a1_0 2.3 MB bioconda
pysocks-1.7.1 | py37hf985489_5 28 KB conda-forge
python-3.7.12 |haf480d7_100_cpython 24.3 MB conda-forge
python-lzo-1.14 | py37h1c4811e_1 18 KB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
scipy-1.7.3 | py37h4e3cf02_0 19.7 MB conda-forge
setuptools-59.8.0 | py37hf985489_1 1.0 MB conda-forge
statsmodels-0.13.2 | py37h032687b_0 10.6 MB conda-forge
typing-extensions-4.2.0 | hd8ed1ab_1 8 KB conda-forge
typing_extensions-4.2.0 | pyha770c72_1 27 KB conda-forge
unicodedata2-14.0.0 | py37h69ee0a8_1 497 KB conda-forge
zipp-3.8.0 | pyhd8ed1ab_0 12 KB conda-forge
------------------------------------------------------------
                                       Total: 148.8 MB

```

The following NEW packages will be INSTALLED:

bcbio-gff bioconda/noarch::bcbio-gff-0.6.9-pyh5e36f6f\_0  
biom-format conda-forge/osx-64::biom-format-2.1.12-py37h49e79e5\_1  
biopython conda-forge/osx-64::biopython-1.79-py37h271585c\_1  
blast bioconda/osx-64::blast-2.6.0-boost1.64\_2  
boost-cpp conda-forge/osx-64::boost-cpp-1.74.0-h8b082ac\_8  
bowtie2 bioconda/osx-64::bowtie2-2.4.5-py37h0f016ca\_2  
brotli conda-forge/osx-64::brotli-1.0.9-h5eb16cf\_7  
brotli-bin conda-forge/osx-64::brotli-bin-1.0.9-h5eb16cf\_7  
brotlipy conda-forge/osx-64::brotlipy-0.7.0-py37h69ee0a8\_1004  
bx-python bioconda/osx-64::bx-python-0.8.13-py37h2b10027\_1  
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4\_4  
c-ares conda-forge/osx-64::c-ares-1.18.1-h0d85af4\_0  
ca-certificates conda-forge/osx-64::ca-certificates-2022.5.18.1-h033912b\_0  
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab\_1  
cached\_property conda-forge/noarch::cached\_property-1.5.2-pyha770c72\_1  
capnproto conda-forge/osx-64::capnproto-0.9.1-h45c0eea\_5  
certifi conda-forge/osx-64::certifi-2022.5.18.1-py37hf985489\_0  
cffi conda-forge/osx-64::cffi-1.15.0-py37h446072c\_0  
charset-normalizer conda-forge/noarch::charset-normalizer-2.0.12-pyhd8ed1ab\_0  
click conda-forge/osx-64::click-8.1.3-py37hf985489\_0  
cmseq bioconda/noarch::cmseq-1.0.4-pyhb7b1952\_0  
cryptography conda-forge/osx-64::cryptography-37.0.2-py37h0169fcd\_0  
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab\_0  
dendropy bioconda/noarch::dendropy-4.5.2-pyh3252c3a\_0  
diamond bioconda/osx-64::diamond-2.0.15-h9d1909e\_0  
fasttree bioconda/osx-64::fasttree-2.1.11-hdcdfbac\_1  
fonttools conda-forge/osx-64::fonttools-4.33.3-py37h994c40b\_0  
freetype conda-forge/osx-64::freetype-2.10.4-h4cff582\_1  
future conda-forge/osx-64::future-0.18.2-py37hf985489\_5  
giflib conda-forge/osx-64::giflib-5.2.1-hbcb3906\_2  
gsl conda-forge/osx-64::gsl-2.7-h93259b0\_0  
h5py conda-forge/osx-64::h5py-3.6.0-nompi\_py37h0ac0de7\_100  
hdf5 conda-forge/osx-64::hdf5-1.12.1-nompi\_ha60fbc9\_104  
htslib bioconda/osx-64::htslib-1.15.1-hc057d7f\_0  
icu conda-forge/osx-64::icu-70.1-h96cf925\_0  
idna conda-forge/noarch::idna-3.3-pyhd8ed1ab\_0  
importlib-metadata conda-forge/osx-64::importlib-metadata-4.11.4-py37hf985489\_0  
iqtree bioconda/osx-64::iqtree-2.2.0.3-h135ad0d\_0  
jpeg conda-forge/osx-64::jpeg-9e-h5eb16cf\_1  
kiwisolver conda-forge/osx-64::kiwisolver-1.4.2-py37h18621fa\_1  
krb5 conda-forge/osx-64::krb5-1.19.3-hb49756b\_0  
lcms2 conda-forge/osx-64::lcms2-2.12-h577c468\_0  
lerc conda-forge/osx-64::lerc-3.0-he49afe7\_0  
libblas conda-forge/osx-64::libblas-3.9.0-14\_osx64\_openblas  
libbrotlicommon conda-forge/osx-64::libbrotlicommon-1.0.9-h5eb16cf\_7  
libbrotlidec conda-forge/osx-64::libbrotlidec-1.0.9-h5eb16cf\_7  
libbrotlienc conda-forge/osx-64::libbrotlienc-1.0.9-h5eb16cf\_7  
libcblas conda-forge/osx-64::libcblas-3.9.0-14\_osx64\_openblas  
libcurl conda-forge/osx-64::libcurl-7.83.1-h372c54d\_0  
libcxx conda-forge/osx-64::libcxx-14.0.4-hc203e6f\_0  
libdeflate conda-forge/osx-64::libdeflate-1.10-h0d85af4\_0  
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f\_2  
libev conda-forge/osx-64::libev-4.33-haf1e3a3\_1  
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4\_5  
libgfortran conda-forge/osx-64::libgfortran-5.0.0-9\_3\_0\_h6c81a4c\_23  
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c\_23  
liblapack conda-forge/osx-64::liblapack-3.9.0-14\_osx64\_openblas  
libnghttp2 conda-forge/osx-64::libnghttp2-1.47.0-h942079c\_0  
libopenblas conda-forge/osx-64::libopenblas-0.3.20-openmp\_hb3cd9ec\_0  
libpng conda-forge/osx-64::libpng-1.6.37-h7cec526\_2  
libssh2 conda-forge/osx-64::libssh2-1.10.0-h52ee1ee\_2  
libtiff conda-forge/osx-64::libtiff-4.4.0-hfca7e8f\_0  
libwebp conda-forge/osx-64::libwebp-1.2.2-h28dabe5\_0  
libwebp-base conda-forge/osx-64::libwebp-base-1.2.2-h0d85af4\_1  
libxcb conda-forge/osx-64::libxcb-1.13-h0d85af4\_1004  
libzlib conda-forge/osx-64::libzlib-1.2.12-h6c3fc93\_0  
llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7\_0  
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7\_1  
lzo conda-forge/osx-64::lzo-2.10-haf1e3a3\_1000  
mafft bioconda/osx-64::mafft-7.505-ha5712d3\_0  
mash bioconda/osx-64::mash-2.3-hf785b45\_2  
matplotlib-base conda-forge/osx-64::matplotlib-base-3.5.2-py37h80cb303\_0  
metaphlan bioconda/noarch::metaphlan-3.0.14-pyhb7b1952\_0  
munkres bioconda/noarch::munkres-1.0.7-py\_1  
muscle bioconda/osx-64::muscle-5.1-hb339e23\_1  
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925\_1  
numpy conda-forge/osx-64::numpy-1.21.6-py37h345d48f\_0  
openjpeg conda-forge/osx-64::openjpeg-2.4.0-h6e7aa92\_1  
openssl conda-forge/osx-64::openssl-1.1.1o-hfe4f2af\_0  
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab\_0  
pandas conda-forge/osx-64::pandas-1.3.4-py37h5b83a90\_1  
patsy conda-forge/noarch::patsy-0.5.2-pyhd8ed1ab\_0  
perl conda-forge/osx-64::perl-5.32.1-2\_h0d85af4\_perl5  
phylophlan bioconda/noarch::phylophlan-3.0.2-py\_0  
pillow conda-forge/osx-64::pillow-9.1.1-py37h1eb1bbc\_1  
pip conda-forge/noarch::pip-22.1.2-pyhd8ed1ab\_0  
pthread-stubs conda-forge/osx-64::pthread-stubs-0.4-hc929b4f\_1001  
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab\_0  
pyopenssl conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab\_0  
pyparsing conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab\_0  
pysam bioconda/osx-64::pysam-0.19.1-py37h64e44a1\_0  
pysocks conda-forge/osx-64::pysocks-1.7.1-py37hf985489\_5  
python conda-forge/osx-64::python-3.7.12-haf480d7\_100\_cpython  
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab\_0  
python-lzo conda-forge/osx-64::python-lzo-1.14-py37h1c4811e\_1  
python\_abi conda-forge/osx-64::python\_abi-3.7-2\_cp37m  
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab\_0  
raxml bioconda/osx-64::raxml-8.2.12-ha5712d3\_4  
readline conda-forge/osx-64::readline-8.1-h05e3726\_0  
requests conda-forge/noarch::requests-2.27.1-pyhd8ed1ab\_0  
samtools bioconda/osx-64::samtools-1.15.1-h9f30945\_0  
scipy conda-forge/osx-64::scipy-1.7.3-py37h4e3cf02\_0  
seaborn conda-forge/noarch::seaborn-0.11.2-hd8ed1ab\_0  
seaborn-base conda-forge/noarch::seaborn-base-0.11.2-pyhd8ed1ab\_0  
setuptools conda-forge/osx-64::setuptools-59.8.0-py37hf985489\_1  
six conda-forge/noarch::six-1.16.0-pyh6c4a22f\_0  
sqlite conda-forge/osx-64::sqlite-3.38.5-hd9f0692\_0  
statsmodels conda-forge/osx-64::statsmodels-0.13.2-py37h032687b\_0  
tbb conda-forge/osx-64::tbb-2020.2-h940c156\_4  
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc\_0  
trimal bioconda/osx-64::trimal-1.4.1-hcd10b59\_6  
typing-extensions conda-forge/noarch::typing-extensions-4.2.0-hd8ed1ab\_1  
typing\_extensions conda-forge/noarch::typing\_extensions-4.2.0-pyha770c72\_1  
unicodedata2 conda-forge/osx-64::unicodedata2-14.0.0-py37h69ee0a8\_1  
urllib3 conda-forge/noarch::urllib3-1.26.9-pyhd8ed1ab\_0  
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab\_0  
xorg-libxau conda-forge/osx-64::xorg-libxau-1.0.9-h35c211d\_0  
xorg-libxdmcp conda-forge/osx-64::xorg-libxdmcp-1.1.3-h35c211d\_0  
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3\_1  
zipp conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab\_0  
zlib conda-forge/osx-64::zlib-1.2.12-h6c3fc93\_0  
zstd conda-forge/osx-64::zstd-1.5.2-ha9df2e0\_1

Proceed ([y]/n)? y

Downloading and Extracting Packages  
pandas-1.3.4 | 11.3 MB | ##################################### | 100%  
typing-extensions-4. | 8 KB | ##################################### | 100%  
statsmodels-0.13.2 | 10.6 MB | ##################################### | 100%  
fonttools-4.33.3 | 1.6 MB | ##################################### | 100%  
pysam-0.19.1 | 2.3 MB | ##################################### | 100%  
python-3.7.12 | 24.3 MB | ##################################### | 100%  
unicodedata2-14.0.0 | 497 KB | ##################################### | 100%  
brotlipy-0.7.0 | 366 KB | ##################################### | 100%  
cryptography-37.0.2 | 1.2 MB | ##################################### | 100%  
importlib-metadata-4 | 33 KB | ##################################### | 100%  
bx-python-0.8.13 | 931 KB | ##################################### | 100%  
future-0.18.2 | 709 KB | ##################################### | 100%  
biopython-1.79 | 2.6 MB | ##################################### | 100%  
h5py-3.6.0 | 1.1 MB | ##################################### | 100%  
typing\_extensions-4. | 27 KB | ##################################### | 100%  
biom-format-2.1.12 | 10.4 MB | ##################################### | 100%  
certifi-2022.5.18.1 | 150 KB | ##################################### | 100%  
scipy-1.7.3 | 19.7 MB | ##################################### | 100%  
click-8.1.3 | 145 KB | ##################################### | 100%  
numpy-1.21.6 | 6.0 MB | ##################################### | 100%  
bowtie2-2.4.5 | 1.4 MB | ##################################### | 100%  
cffi-1.15.0 | 218 KB | ##################################### | 100%  
kiwisolver-1.4.2 | 61 KB | ##################################### | 100%  
metaphlan-3.0.14 | 237 KB | ##################################### | 100%  
setuptools-59.8.0 | 1.0 MB | ##################################### | 100%  
matplotlib-base-3.5. | 7.4 MB | ##################################### | 100%  
zipp-3.8.0 | 12 KB | ##################################### | 100%  
python-lzo-1.14 | 18 KB | ##################################### | 100%  
pillow-9.1.1 | 44.5 MB | ##################################### | 100%  
pysocks-1.7.1 | 28 KB | ##################################### | 100%  
python\_abi-3.7 | 4 KB | ##################################### | 100%  
Preparing transaction: done  
Verifying transaction: done  
Executing transaction: done

# 

# To activate this environment, use

# 

# $ conda activate mpa

# 

# To deactivate an active environment, use

# 

# $ conda deactivate

(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % cd  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % mkdir -p db/metaphlan\_databases  
(base) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % conda activate mpa  
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % metaphlan --install --bowtie2db ~/db/metaphlan\_databases

Downloading [http://cmprod1.cibio.unitn.it/biobakery3/metaphlan\_databases/mpa\_latest](http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest)  
Downloading file of size: 0.00 MB  
0.01 MB 31507.69 % 53.19 MB/sec 0 min -0 sec  
Downloading MetaPhlAn database  
Please note due to the size this might take a few minutes

Downloading [http://cmprod1.cibio.unitn.it/biobakery3/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.tar](http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.tar)  
Downloading file of size: 366.62 MB  
366.62 MB 100.00 % 7.71 MB/sec 0 min -0 sec  
Downloading [http://cmprod1.cibio.unitn.it/biobakery3/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.md5](http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.md5)  
Downloading file of size: 0.00 MB  
0.01 MB 12800.00 % 35.01 MB/sec 0 min -0 sec

Decompressing /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.fna.bz2 into /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.fna

Building Bowtie2 indexes  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.3.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.3.bt2  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.4.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.4.bt2  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.1.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.1.bt2  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.2.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.2.bt2  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.rev.1.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.rev.1.bt2  
Renaming /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.rev.2.bt2.tmp to /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.rev.2.bt2  
Removing uncompress database /Users/stephaniegetto/db/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.fna

Download complete  
The database is installed  
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % mkdir metaphlan\_analysis  
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 ~ % cd metaphlan\_analysis  
(mpa) stephaniegetto@Stephanies-MacBook-Pro-3 metaphlan\_analysis % curl -LO [https://github.com/biobakery/biobakery/raw/master/demos/biobakery\_demos/data/metaphlan3/input/SRS014476-Supragingival\_plaque.fasta.gz](https://github.com/biobakery/biobakery/raw/master/demos/biobakery_demos/data/metaphlan3/input/SRS014476-Supragingival_plaque.fasta.gz)  
% Total % Received % Xferd Average Speed Time Time Time Current  
Dload Upload Total Spent Left Speed  
100 192k 0 192k 0 0 360k 0 --:–:-- --:–:-- --:–:-- 365k

I have run this sample in other programs and gotten some results, so I don’t think it’s bad data… any ideas?

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [June 7, 2022, 12:38pm UTC](https://forum.biobakery.org/t/analysis-says-100-unknown/3681/2 "2022-06-07T12:38:30Z")

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Hi @sgetto  
From the results you are showing here it seems that metaphlan was not able to map any read against the markers database. From the `bowtie2out` file, you can see that metaphlan was only able to use 175 reads from your fastq file. Is the `9-8_R1.fastq` file containing only 175 reads? and in case it contains more reads, are the reads short in length (\<70nt)?