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jolobito / SPdel

Comparing species delimitation methods and statistics for DNA Barcoding data sets
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asap not found? #47

Open ymilesz opened 11 months ago

ymilesz commented 11 months ago

Hi I am trying to run the test data with SPdel, but I am getting the following error:

Traceback (most recent call last): File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 1202, in main() File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 1193, in main run(fasta,a,tree,CODE,dis,niter,sample,burnin,gen,sp,specList,n_ind,nocons,XList,PTPList,bPTPList,GMYCList,CompList,diagnostic) File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 947, in run distances=run_ASAP(basepath,inputs,gen,sp,dis) File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 845, in run_ASAP subprocess.call(['asap', '-d', d, '-o',os.path.join(basepath, 'ASAP'), file]) File "/home/zhangy/miniconda3/envs/spdel/lib/python3.10/subprocess.py", line 345, in call with Popen(*popenargs, **kwargs) as p: File "/home/zhangy/miniconda3/envs/spdel/lib/python3.10/subprocess.py", line 971, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/home/zhangy/miniconda3/envs/spdel/lib/python3.10/subprocess.py", line 1863, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'asap'

Also the example in the readme file is outdated, if possible please update that to make following along easier.

Thanks,

Miles

maycol1551 commented 11 months ago

example in the readme file is outdated, if possible please update that to make following along

I encountered the same issue. In the end I used the -X option to add the results from ASAP and ABGD in a csv

jolobito commented 11 months ago

Hi @ymilesz . Thanks for use SPdel. The README is now updated! To find exactly the error I need some information:

  1. Are you using the commnad line or jupyter version?
  2. What is your OS?

It seems like the asap binary was not correctly instaled for some reason. I noted that in some computer the antivirus could block the installation.

ymilesz commented 11 months ago

Hi Jorge,

  1. I am using the command line version
  2. It is a Linux cluster, CentOS 8.5 perhaps?
jolobito commented 11 months ago

Can you check the content of this folder /home/zhangy/miniconda3/envs/spdel/bin ??

ymilesz commented 11 months ago

2to3 2to3-3.10 abgd_linux asap_linux aserver assistant attr autopoint balsam bPTP.py bunzip2 bzcat bzcmp bzdiff bzegrep bzfgrep bzgrep bzip2 bzip2recover bzless bzmore cairo-trace canbusutil captoinfo certutil cjpeg clear compile_et c_rehash cups-config cwebp dbus-cleanup-sockets dbus-daemon dbus-launch dbus-monitor dbus-run-session dbus-send dbus-test-tool dbus-update-activation-environment dbus-uuidgen derb designer Diagnoser.py djpeg dumpsexp dwebp envsubst ete3 f2py fc-cache fc-cat fc-conflist fc-list fc-match fc-pattern fc-query fc-scan fc-validate fixqt4headers.pl flac fonttools freetype-config futurize gapplication gdbus gdbus-codegen genbrk gencfu gencnval gendict genrb getfattr gettext gettextize gettext.sh gif2rgb gif2webp gifbuild gifclrmp giffix giftext giftool gio gio-querymodules glib-compile-resources glib-compile-schemas glib-genmarshal glib-gettextize glib-mkenums GMYC.py gobject-query gpg-error gpgrt-config gresource gsettings gss-client gst-device-monitor-1.0 gst-discoverer-1.0 gst-inspect-1.0 gst-launch-1.0 gst-play-1.0 gst-stats-1.0 gst-typefind-1.0 gtester gtester-report hb-info hb-ot-shape-closure hb-shape hb-subset hb-view hmac256 iconv icu-config icuexportdata icuinfo idle3 idle3.10 img2webp infocmp infotocap ippeveprinter ipptool ipython ipython3 jlpm jpegtran jpgicc jsonpointer jsonschema jupyter jupyter-dejavu jupyter-events jupyter-execute jupyter-kernel jupyter-kernelspec jupyter-lab jupyter-labextension jupyter-labhub jupyter-migrate jupyter-nbconvert jupyter-notebook jupyter-run jupyter-server jupyter-troubleshoot jupyter-trust k5srvutil kadmin kaleido KaleidoApp kdestroy keyctl kinit klist kpasswd krb5-config ksu kswitch ktutil kvno lame lconvert libdeflate-gunzip libdeflate-gzip libgcrypt-config libpng16-config libpng-config linguist linkicc lprodump lrelease lrelease-pro lupdate lupdate-pro lz4 lz4c lz4cat lzcat lzcmp lzdiff lzegrep lzfgrep lzgrep lzless lzma lzmadec lzmainfo lzmore makeconv mathjax-path meshdebug metaflac moc mpg123 mpg123-id3dump mpg123-strip mpicalc mptp_linux msgattrib msgcat msgcmp msgcomm msgconv msgen msgexec msgfilter msgfmt msggrep msginit msgmerge msgunfmt msguniq ncurses6-config ncursesw6-config ngettext normalizer nspr-config nss-config openssl opj_compress opj_decompress opj_dump out123 pacat pactl padsp pa-info pamon paplay parec parecord pasteurize pcre2-config pcre2grep pcre2_jit_test pcre2posix_test pcre2test pg_config pip pip3 pixeltool pk12util pkgdata pngfix png-fix-itxt prichunkpng pricolpng priditherpng priforgepng prigreypng pripalpng pripamtopng priplan9topng pripnglsch pripngtopam prirowpng priweavepng psicc PTP.py pybabel pycache pydoc pydoc3 pydoc3.10 pyftmerge pyftsubset pygmentize pyjson5 pylupdate5 pyrcc5 python python3 python3.1 python3.10 python3.10-config python3-config pyuic5 qcollectiongenerator qdbus qdbuscpp2xml qdbusviewer qdbusxml2cpp qdistancefieldgenerator qdoc qgltf qhelpgenerator qlalr qmake qml qmlcachegen qmleasing qmlformat qmlimportscanner qmllint qmlmin qmlplugindump qmlpreview qmlprofiler qmlscene qmltestrunner qmltime qmltyperegistrar qscxmlc qtattributionsscanner qt.conf qtdiag qtpaths qtplugininfo qvkgen qwebengine_convert_dict rcc rdjpgcom recode-sr-latin repc reset sclient send2trash setfattr sim_client sip-build sip-distinfo sip-install sip-module sip-sdist sip-wheel sndfile-cmp sndfile-concat sndfile-convert sndfile-deinterleave sndfile-info sndfile-interleave sndfile-metadata-get sndfile-metadata-set sndfile-play sndfile-salvage SPdel.py sqlite3 sqlite3_analyzer summary.py syncqt.pl tabs tclsh tclsh8.6 tic tiffcp tiffdump tiffinfo tiffset tiffsplit tificc tjbench toe tput tracegen transicc tset ttx uic unlz4 unlzma unxz unzstd uuclient webpinfo webpmux wheel wish wish8.6 wrjpgcom wsdump x86_64-conda_cos6-linux-gnu-ld x86_64-conda-linux-gnu-ld xgettext xkbcli xml2-config xmlcatalog xmllint xmlpatterns xmlpatternsvalidator xmlwf xslt-config xsltproc xz xzcat xzcmp xzdec xzdiff xzegrep xzfgrep xzgrep xzless xzmore yat2m zstd zstdcat zstdgrep zstdless zstdmt

jolobito commented 11 months ago

Try running 

asap -h

or

home/zhangy/miniconda3/envs/spdel/bin/asap_linux -h

or

chmod +x home/zhangy/miniconda3/envs/spdel/bin/asap_linux
home/zhangy/miniconda3/envs/spdel/bin/asap_linux -h

any of these works?

ymilesz commented 11 months ago

first one didn't work, second asked for permission, so after chmod +x I got the following:

asap_linux: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by asap_linux)

jolobito commented 7 months ago

Hi @ymilesz We update the SPdel for this issue. Please download and install again. Let us know if the issue persists or if it is now resolved.

ymilesz commented 7 months ago

Hi I am getting different errors now after reinstalling SPdel:

Following the example I did: SPdel.py path/Megaleporinus_COI.fasta -n -A -S -P -T -G -t path/Megaleporinus_tree.nwk

and I got 

File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 1246, in <module>
    main()
  File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 1237, in main
    run(fasta,a,tree,CODE,dis,niter,sample,burnin,gen,sp,specList,n_ind,nocons,XList,PTPList,bPTPList,GMYCList,CompList,diagnostic)
  File "/home/zhangy/miniconda3/envs/spdel/bin/SPdel.py", line 986, in run
    distances.plot_freq(cmd=True)
  File "/home/zhangy/miniconda3/envs/spdel/lib/python3.10/site-packages/spdelib/Matrian.py", line 231, in plot_freq
    max_counts_tra = max(counts_tra)
ValueError: max() arg is an empty sequence
Ulises-Rosas commented 7 months ago

Did you provide a complete location for the Megaleporinus_COI.fasta file? i.e., did you change path in path/Megaleporinus_COI.fasta for the correct path?

ymilesz commented 7 months ago

Hi yes I did:

python SPdel.py /scratch/usda_sel/zhangy/SPdel/data/Megaleporinus/Megaleporinus_COI.fasta -n -A -S -P -T -G -t /scratch/usda_sel/zhangy/SPdel/data/Megaleporinus/Megaleporinus_tree.nwk

jolobito commented 7 months ago

Hi @ymilesz. It seems to be a issue with abgd compilation for linux. I updated again witha new binary. Please reinstall and check if the issue is solved. Thanks for help us to improve SPdel!

ymilesz commented 7 months ago

Hi I am still getting that same error?

Traceback (most recent call last): File "/scratch/usda_sel/zhangy/SPdel/SPdel.py", line 1246, in main() File "/scratch/usda_sel/zhangy/SPdel/SPdel.py", line 1237, in main run(fasta,a,tree,CODE,dis,niter,sample,burnin,gen,sp,specList,n_ind,nocons,XList,PTPList,bPTPList,GMYCList,CompList,diagnostic) File "/scratch/usda_sel/zhangy/SPdel/SPdel.py", line 986, in run distances.plot_freq(cmd=True) File "/scratch/usda_sel/zhangy/SPdel/spdelib/Matrian.py", line 231, in plot_freq max_counts_tra = max(counts_tra) ValueError: max() arg is an empty sequence

jolobito commented 7 months ago

HI @ymilesz

  1. Can you try:

python SPdel.py /scratch/usda_sel/zhangy/SPdel/data/Megaleporinus/Megaleporinus_COI.fasta -n -S -P -T -G -t /scratch/usda_sel/zhangy/SPdel/data/Megaleporinus/Megaleporinus_tree.nwk

without -A to test if ABGD is the source of the issue.

  1. Also, check in the Megaleporinus_COI.rec.spart file in the ABGD folder (should be in SPdel/data/Megaleporinus/ ) the line after "[Barcode gap distance :]". Shoul be shomething like:

[1.00e-03 / 1.67e-03 / 2.78e-03 / 4.64e-03 / 7.74e-03 / 1.29e-02 / 2.15e-02 / 3.593814e-02]

Thanks

ymilesz commented 7 months ago

Hello again

  1. It did finish without -A
  2. They all said 0

begin spart; Project_name = Megaleporinus_COI; Date = 1969-12-31T19:00:00; N_spartitions = 7 : Megaleporinus_COI_abgd_rec_1 / Megaleporinus_COI_abgd_rec_2 / Megaleporinus_COI_abgd_rec_3 / Megaleporinus_COI_abgd_rec_4 / Megaleporinus_COI_abgd_rec_5 / Megaleporinus_COI_abgd_rec_6 / Megaleporinus_COI_abgd_rec_7; N_individuals = 116 / 116 / 116 / 116 / 116 / 116 / 116; N_subsets = 27 / 27 / 19 / 18 / 16 / 16 / 15; [Generated by ABGD with Distance K80 Kimura / MinSlope = 1.500000] [Barcode gap distance :] [0.00e+00 / 0.00e+00 / 0.00e+00 / 0.00e+00 / 0.00e+00 / 0.00e+00 / 0.000000e+00] [WARNING: The sample names below may have been changed to fit SPART specification (only alphanumeric characters and _ )]