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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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python -m jcvi.compara.catalog ortholog grape peach --no_strip_names ERROR Set text.usetex=False. Font styles may be inconsistent. #393

Closed NINGCHINA closed 1 year ago

NINGCHINA commented 3 years ago

I run jcvi on the macos when run the command 'python -m jcvi.compara.catalog ortholog grape peach --no_strip_names' ,encounter an error 'ERROR Set text.usetex=False. Font styles may be inconsistent.'

PAMorin commented 3 years ago

I'm also trying to use this for the first time, on a Linux system, and run into the same error. I thought it was a problem with using different data files (from cetacean genomes), so I went to the example for grape/peach and followed the instructions. When I get the synteny search, I get this error:

python -m jcvi.compara.catalog ortholog grape peach --no_strip_names [10:51:29] ERROR Set text.usetex=False. Font styles may be inconsistent. base.py:403 DEBUG lastdb peach peach.cds base.py:1184 /bin/bash: lastdb: command not found DEBUG lastal -u 0 -P 20 -i3G -f BlastTab peach grape.cds base.py:1184 ./grape.peach.last /bin/bash: lastal: command not found DEBUG Assuming --qbed=grape.bed --sbed=peach.bed synteny.py:499 DEBUG Load file grape.bed base.py:34 [10:51:30] DEBUG Load file peach.bed base.py:34 DEBUG Load BLAST file grape.peach.last (total 0 lines) blastfilter.py:47 DEBUG Load file grape.peach.last base.py:34 DEBUG running the cscore filter (cscore>=0.70) .. blastfilter.py:108 DEBUG after filter (0->0) .. blastfilter.py:111 DEBUG running the local dups filter (tandem_Nmax=10) .. blastfilter.py:116 DEBUG after filter (0->0) .. blastfilter.py:156 DEBUG Assuming --qbed=grape.bed --sbed=peach.bed synteny.py:499 DEBUG Load file grape.bed base.py:34 DEBUG Load file peach.bed base.py:34 [10:51:31] DEBUG Load file grape.peach.last.filtered base.py:34 DEBUG A total of 0 BLAST imported from grape.peach.last.filtered. synteny.py:387 DEBUG Chaining distance = 20 synteny.py:1931 DEBUG Load file grape.peach.anchors base.py:34 DEBUG A total of 0 anchor was found. Aborted. synteny.py:1480 Traceback (most recent call last): File "/usr/lib64/python3.6/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/usr/lib64/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/compara/catalog.py", line 947, in main() File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/compara/catalog.py", line 78, in main p.dispatch(globals()) File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/apps/base.py", line 110, in dispatch globalsaction File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/compara/catalog.py", line 715, in ortholog scan(dargs) File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/compara/synteny.py", line 1948, in scan summary([anchor_file]) File "/home/pmorin/programs/python/lib64/python3.6/site-packages/jcvi/compara/synteny.py", line 1481, in summary raise ValueError("A total of 0 anchor was found. Aborted.") ValueError: A total of 0 anchor was found. Aborted.

tanghaibao commented 3 years ago

@PAMorin

There is a line saying:

/bin/bash: lastal: command not found

You'll need to install LAST (https://gitlab.com/mcfrith/last) and place binaries lastal and lastdb on your PATH.

Haibao

wangtaohhh commented 3 years ago

I run jcvi on the macos when run the command 'python -m jcvi.compara.catalog ortholog grape peach --no_strip_names' ,encounter an error 'ERROR Set text.usetex=False. Font styles may be inconsistent.'

Hi, @NINGCHINA. I solved this problem by installing latex on Ubuntu. You may have a try.

pauloizquierdo commented 3 years ago

I am running 'python -m jcvi.compara.catalog ortholog grape peach --no_strip_names' and I got this error:

ERROR Fall back to Python implementation of BlastLine blast.py:28 ERROR Set text.usetex=False. Font styles may be inconsistent. base.py:402

and also the following

Traceback (most recent call last): File "/Users/paulo/miniconda3/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/Users/paulo/miniconda3/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 947, in main() File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 78, in main p.dispatch(globals()) File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/apps/base.py", line 110, in dispatch globalsaction File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/compara/catalog.py", line 715, in ortholog scan(dargs) File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/compara/synteny.py", line 1948, in scan summary([anchor_file]) File "/Users/paulo/.local/lib/python3.9/site-packages/jcvi/compara/synteny.py", line 1481, in summary raise ValueError("A total of 0 anchor was found. Aborted.") ValueError: A total of 0 anchor was found. Aborted.

Do I have to change the python version?

songjuntae2022 commented 3 years ago

I solved it by removing texlive-core from conda and getting texlive with apt-get.

conda remove -n myenv texlive-core
sudo apt-get install texlive
tararickman commented 2 years ago

I am getting this same error when I execute python -m jcvi.compara.catalog ortholog clementine sweet_orange --no_strip_names on a Linux system. I am using two citrus species retrieved from Phytozome and following the tutorial. I have the dependencies installed and PATHs updated in my .bashrc file. I also followed the recommendation of removing texlive-core from my base conda environment and installed texlive but the error persists with no change:

(base) [trickman@centaur 20211117_mcscan]$ python -m jcvi.compara.catalog ortholog clementine sweet_orange --no_strip_names
[17:21:02] ERROR    Set text.usetex=False. Font styles may be inconsistent.                                                                                                                           base.py:402
           DEBUG    lastdb sweet_orange sweet_orange.cds                                                                                                                                             base.py:1184
[17:22:00] DEBUG    lastal -u 0 -P 96 -i3G -f BlastTab sweet_orange clementine.cds >./clementine.sweet_orange.last                                                                                   base.py:1184
lastal: I was installed here with multi-threading disabled
           DEBUG    Assuming --qbed=clementine.bed --sbed=sweet_orange.bed                                                                                                                         synteny.py:499
           DEBUG    Load file `clementine.bed`                                                                                                                                                         base.py:34
           DEBUG    Load file `sweet_orange.bed`                                                                                                                                                       base.py:34
           DEBUG    Load BLAST file `clementine.sweet_orange.last` (total 0 lines)                                                                                                              blastfilter.py:46
           DEBUG    Load file `clementine.sweet_orange.last`                                                                                                                                           base.py:34
           DEBUG    running the cscore filter (cscore>=0.70) ..                                                                                                                                blastfilter.py:108
           DEBUG    after filter (0->0) ..                                                                                                                                                     blastfilter.py:110
           DEBUG    running the local dups filter (tandem_Nmax=10) ..                                                                                                                          blastfilter.py:115
           DEBUG    after filter (0->0) ..                                                                                                                                                     blastfilter.py:155
           DEBUG    Assuming --qbed=clementine.bed --sbed=sweet_orange.bed                                                                                                                         synteny.py:499
[17:22:01] DEBUG    Load file `clementine.bed`                                                                                                                                                         base.py:34
           DEBUG    Load file `sweet_orange.bed`                                                                                                                                                       base.py:34
           DEBUG    Load file `clementine.sweet_orange.last.filtered`                                                                                                                                  base.py:34
           DEBUG    A total of 0 BLAST imported from `clementine.sweet_orange.last.filtered`.                                                                                                      synteny.py:386
           DEBUG    Chaining distance = 20                                                                                                                                                        synteny.py:1931
           DEBUG    Load file `clementine.sweet_orange.anchors`                                                                                                                                        base.py:34
           DEBUG    A total of 0 anchor was found. Aborted.                                                                                                                                       synteny.py:1480
Traceback (most recent call last):
  File "/home/trickman/miniconda3/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/trickman/miniconda3/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 947, in <module>
    main()
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 78, in main
    p.dispatch(globals())
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/apps/base.py", line 110, in dispatch
    globals[action](sys.argv[2:])
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/compara/catalog.py", line 715, in ortholog
    scan(dargs)
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/compara/synteny.py", line 1948, in scan
    summary([anchor_file])
  File "/home/trickman/miniconda3/lib/python3.8/site-packages/jcvi/compara/synteny.py", line 1481, in summary
    raise ValueError("A total of 0 anchor was found. Aborted.")
ValueError: A total of 0 anchor was found. Aborted.

Are there any other possible solutions to this error?

Thank you for this tool and for taking the time to read this!

tanghaibao commented 2 years ago

@tararickman

Looks like lastal step failed, since you had an empty LAST output.

DEBUG    Load BLAST file `clementine.sweet_orange.last` (total 0 lines)

Are you able to run this command?

lastal -u 0 -P 96 -i3G -f BlastTab sweet_orange clementine.cds >./clementine.sweet_orange.last

lastal: I was installed here with multi-threading disabled

Looks like the LAST was complaining that it doesn't support multiple threads.

Haibao

tararickman commented 2 years ago

I am able to run the command with no errors just the same multi-threading message:

(base) [trickman@centaur 20211117_mcscan]$ lastal -u 0 -P 96 -i3G -f BlastTab sweet_orange clementine.cds >./clementine.sweet_orange.last
lastal: I was installed here with multi-threading disabled

Do I need to change something about how I am installing LAST? I was not prompted to indicate if multiple threads should/shouldn't be supported at any point during the installation.

wyim-pgl commented 2 years ago

https://github.com/tanghaibao/jcvi/issues/440

Mengzhuo-Zheng commented 2 years ago

Hi, have you solve the problem? I have the same problem and I have installed the latex by pip, but I cannnot solve it.

TAKosch commented 2 years ago

Has this issue been resolved yet? I am also getting the same error when running the example:

python -m jcvi.compara.catalog ortholog grape peach --no_strip_names INFO Set text.usetex=False. Font styles may be inconsistent.

pauloizquierdo commented 2 years ago

Hi,

The problem was LaTex,... and after installing LaTex I was getting the same error, so I restarted the computer and it worked. I hope this helps.

On Wed, Sep 28, 2022 at 9:32 PM Tiffany Kosch @.***> wrote:

Has this issue been resolved yet? I am also getting the same error when running the example:

python -m jcvi.compara.catalog ortholog grape peach --no_strip_names INFO Set text.usetex=False. Font styles may be inconsistent.

— Reply to this email directly, view it on GitHub https://github.com/tanghaibao/jcvi/issues/393#issuecomment-1261634839, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKE3XHDD5G7AN5F2YBDM4ZTWATWRDANCNFSM5BGWT6ZA . You are receiving this because you commented.Message ID: @.***>

-- ____ Paulo Izquierdo Graduate Research Assistant Plant Breeding, Genetics and Biotechnology (PBGB) Department of Plant, Soil, and Microbial Science Michigan State University Plant and Soil Science Building 1066 Bogue Street, East Lansing, MI 48823. Room A 494J

Mengzhuo-Zheng commented 2 years ago

Hello, it is a pitty that I had not resolve this problem in my linux hosts. However, you can try to install and pull down the related 'docker' in your windows hosts and I had done it successfully. Good luck!

TAKosch commented 2 years ago

Hello Paolo,

Thanks for your advice. I managed to solve the latex issue and generate the anchor files, but now I'm getting errors at the dotplot step of the tutorial. Have you managed to successfully run the entire tutorial using an anaconda installation?

Cheers, Tiffany

On Thu, Sep 29, 2022 at 11:38 AM Paulo Izquierdo @.***> wrote:

Hi,

The problem was LaTex,... and after installing LaTex I was getting the same error, so I restarted the computer and it worked. I hope this helps.

On Wed, Sep 28, 2022 at 9:32 PM Tiffany Kosch @.***> wrote:

Has this issue been resolved yet? I am also getting the same error when running the example:

python -m jcvi.compara.catalog ortholog grape peach --no_strip_names INFO Set text.usetex=False. Font styles may be inconsistent.

— Reply to this email directly, view it on GitHub https://github.com/tanghaibao/jcvi/issues/393#issuecomment-1261634839, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKE3XHDD5G7AN5F2YBDM4ZTWATWRDANCNFSM5BGWT6ZA

. You are receiving this because you commented.Message ID: @.***>

-- ____ Paulo Izquierdo Graduate Research Assistant Plant Breeding, Genetics and Biotechnology (PBGB) Department of Plant, Soil, and Microbial Science Michigan State University Plant and Soil Science Building 1066 Bogue Street, East Lansing, MI 48823. Room A 494J

— Reply to this email directly, view it on GitHub https://github.com/tanghaibao/jcvi/issues/393#issuecomment-1261637855, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHHOQVTBAK3KK3GOG4QYLTWATXIBANCNFSM5BGWT6ZA . You are receiving this because you commented.Message ID: @.***>

-- Tiffany A. Kosch Research Fellow One Health Research Group University of Melbourne Werribee, VIC, Australia Tel: +61 04 5108 4881 Email: @. @.>

TAKosch commented 2 years ago

Thanks for your response. I may try the docker next. JVCI seems to have many glitches. I finally managed to results this text issue and now another one has come up.

Cheers, Tiffany

On Thu, Sep 29, 2022 at 11:52 AM BioZMZ @.***> wrote:

Hello, it is a pitty that I had not resolve this problem in my linux hosts. However, you can try to install and pull down the related 'docker' in your windows hosts and I had done it successfully. Good luck!

— Reply to this email directly, view it on GitHub https://github.com/tanghaibao/jcvi/issues/393#issuecomment-1261644770, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHHOQWGNOLSIN3MQ5KIHTDWATY4NANCNFSM5BGWT6ZA . You are receiving this because you commented.Message ID: @.***>

-- Tiffany A. Kosch Research Fellow One Health Research Group University of Melbourne Werribee, VIC, Australia Tel: +61 04 5108 4881 Email: @. @.>

wyim-pgl commented 2 years ago

Use conda conda create -y -n jcvi-c conda-forge -c bioconda numpy last=1260 jcvi=1.1.19 emboss bedtools more-itertools texlive-core=20210325