raspir error - Githubissues

LisaHollstein commented 2 years ago

Ilona and I have the same issue with raspir. It starts but creates no output files without giving any error messages or any other helpful output.

colindaven commented 2 years ago

Ok.

Which input data ?
Are the relevant files linked into the raspir work folder ?
Does the raspir_fileprep complete successfully ? See work
Are there enough reads in the sample for raspir ?

This is strange, because it has been working fine this side for weeks with the test fastqs from https://github.com/colindaven/ref_testing

colindaven commented 2 years ago

I just ran a lot of tests last night, and got no failures at all ... see bottom. Output files are also full.

@LisaHollstein if you set this forraspir and raspir_fileprep you'll get at least the working dir to navigate to so you can check for errors. I have a feeling it might be something in the haybaler env used by raspir.

errorStrategy 'terminate'

Please check haybaler env like this

conda activate haybaler
conda list

--> does yours look similar ? Identical ? Please export to file, and yours too, then compare with vimdiff x.txt y.txt

# packages in environment at /home/hpc/davenpor/programs/miniconda3/envs/haybaler:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
appdirs                   1.4.4                    pypi_0    pypi
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
biopython                 1.78                     pypi_0    pypi
black                     20.8b1                   pypi_0    pypi
blas                      1.0                         mkl
bzip2                     1.0.8                h516909a_3    conda-forge
c-ares                    1.16.1               h516909a_3    conda-forge
ca-certificates           2021.1.19            h06a4308_1
certifi                   2020.12.5        py37h89c1867_1    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
fastcache                 1.1.0            py37h4abf009_2    conda-forge
ffmpeg                    4.3.1                h3215721_1    conda-forge
freetype                  2.10.2               he06d7ca_0    conda-forge
gmp                       6.2.0                h58526e2_4    conda-forge
gmpy2                     2.1.0b1          py37hcb968a4_1    conda-forge
gnutls                    3.6.13               h79a8f9a_0    conda-forge
importlib-metadata        2.0.0            py37hc8dfbb8_0    conda-forge
importlib_metadata        2.0.0                         1    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intel-openmp              2022.0.1          h06a4308_3633
jack                      0.125.0           hf484d3e_1001    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kiwisolver                1.2.0            py37h99015e2_1    conda-forge
krb5                      1.17.1               hfafb76e_3    conda-forge
lame                      3.100             h14c3975_1001    conda-forge
lcms2                     2.11                 hcbb858e_1    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_8    conda-forge
libblas                   3.8.0                    21_mkl    conda-forge
libcblas                  3.8.0                    21_mkl    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libdb                     6.1.26                        0    bioconda
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0
libgfortran-ng            7.5.0               h14aa051_20    conda-forge
libgfortran4              7.5.0               h14aa051_20    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.8.0                    21_mkl    conda-forge
libnghttp2                1.41.0               h8cfc5f6_2    conda-forge
libopenblas               0.3.10          pthreads_hb3c22a3_5    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0
libtiff                   4.1.0                h4f3a223_6    conda-forge
libwebp-base              1.1.0                h36c2ea0_3    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
mad                       0.15.1b              he1b5a44_0    conda-forge
mkl                       2020.2                      256  
more-itertools            8.6.0              pyhd8ed1ab_0    conda-forge
mpc                       1.1.0             h04dde30_1009    conda-forge
mpfr                      4.0.2                he80fd80_1    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
mypy-extensions           0.4.3                    pypi_0    pypi
mysql-connector           2.2.9                    pypi_0    pypi
mysql-connector-python    8.0.21                   pypi_0    pypi
mysql-connector-python-rf 2.2.2                    pypi_0    pypi
ncurses                   6.2                  h58526e2_4    conda-forge
nettle                    3.4.1             h1bed415_1002    conda-forge
numpy                     1.19.1           py37h7ea13bd_2    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openh264                  2.1.1                h8b12597_0    conda-forge
openssl                   1.1.1i               h27cfd23_0  
packaging                 20.9               pyh44b312d_0    conda-forge
pandas                    1.1.1            py37h3340039_0    conda-forge
pathspec                  0.8.0                    pypi_0    pypi
pillow                    7.2.0            py37h718be6c_2    conda-forge
pip                       20.2.2                     py_0    conda-forge
pluggy                    0.13.1           py37h89c1867_4    conda-forge
portaudio                 19.6.0               h1398938_3    conda-forge
protobuf                  3.13.0                   pypi_0    pypi
py                        1.10.0             pyhd3deb0d_0    conda-forge
pyaudio                   0.2.11          py37h8f50634_1002    conda-forge
pydub                     0.23.1                     py_0    conda-forge
pyparsing                 2.4.7              pyhd8ed1ab_1    conda-forge
pysam                     0.16.0.1         py37hc334e0b_1    bioconda
pytaxonkit                0.7.2                      py_0    bioconda
pytest                    6.2.2            py37h89c1867_0    conda-forge
python                    3.7.7                hcff3b4d_5  
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2020.1             pyh9f0ad1d_0    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
regex                     2020.10.15               pypi_0    pypi
scipy                     1.5.2            py37h8911b10_2    conda-forge
setuptools                49.6.0           py37h89c1867_3    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sox                       14.4.2            h27f72bc_1013    conda-forge
sqlite                    3.32.3               h4cf870e_1    conda-forge
sympy                     1.6.2            py37h89c1867_1    conda-forge
taxonkit                  0.7.2                h9ee0642_1    bioconda
tk                        8.6.10               h21135ba_1    conda-forge
toml                      0.10.1             pyh9f0ad1d_0    conda-forge
tornado                   6.0.4            py37h8f50634_2    conda-forge
typed-ast                 1.4.1                    pypi_0    pypi
typing-extensions         3.7.4.3                  pypi_0    pypi
wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
x264                      1!152.20180806       h14c3975_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zipp                      3.4.0                      py_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge


[3f/491da7] Submitted process > wochenende (ERR9809365_R1.fastq)
[da/403e8f] Submitted process > wochenende (public_mock_qsm_R1.fastq)
[38/714c47] Submitted process > wochenende (ERR9809371_R1.fastq)
[51/a45e78] Submitted process > wochenende (ERR9809360_R1.fastq)
[60/919fa6] Submitted process > wochenende (public_mock_qsm3_R1.fastq)
[35/5812de] Submitted process > wochenende (DRR_sm_R1.fastq)
[ed/c55510] Submitted process > plots (public_mock_qsm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[bd/a887bd] Submitted process > growth_rate (public_mock_qsm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[bf/94b420] Submitted process > reporting (public_mock_qsm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[4b/e49279] Submitted process > raspir_fileprep (public_mock_qsm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[0e/d8490c] Submitted process > reporting (ERR9809371_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[f6/b34db7] Submitted process > plots (ERR9809371_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[b1/35006c] Submitted process > raspir_fileprep (ERR9809371_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[fb/354d96] Submitted process > growth_rate (ERR9809371_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[db/b4d3e8] Submitted process > raspir (public_mock_qsm_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[d9/9e91c2] Submitted process > raspir (ERR9809371_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[2f/eb0a2a] Submitted process > reporting (public_mock_qsm3_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[19/4b6524] Submitted process > raspir_fileprep (public_mock_qsm3_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[cf/ec2858] Submitted process > plots (public_mock_qsm3_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[03/0d42ea] Submitted process > growth_rate (public_mock_qsm3_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[e4/4345a6] Submitted process > reporting (ERR9809360_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[cb/de617f] Submitted process > plots (ERR9809360_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[98/5ab41d] Submitted process > raspir_fileprep (ERR9809360_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[4a/5d2801] Submitted process > growth_rate (ERR9809360_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[8a/29fde7] Submitted process > raspir (public_mock_qsm3_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[9a/c54078] Submitted process > reporting (DRR_sm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[34/95c8bd] Submitted process > plots (DRR_sm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[57/eaaaa9] Submitted process > raspir_fileprep (DRR_sm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[73/80afcc] Submitted process > growth_rate (DRR_sm_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[54/8c2b65] Submitted process > raspir (DRR_sm_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[61/d0aadf] Submitted process > raspir (ERR9809360_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[63/c993a7] Submitted process > plots (ERR9809365_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[c5/defbb1] Submitted process > growth_rate (ERR9809365_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[2b/8ad925] Submitted process > raspir_fileprep (ERR9809365_R1.ndp.trm.s.mm.dup.mq30.calmd.bam)
[26/51b4e7] Submitted process > reporting (ERR9809365_R1.ndp.trm.s.mm.dup.mq30.calmd.bam.txt)
[24/f82deb] Submitted process > raspir (ERR9809365_R1.ndp.trm.s.mm.dup.mq30.calmd.raspir.csv)
[c9/1bf926] Submitted process > haybaler (haybaler_input)

LisaHollstein commented 2 years ago

* Which input data ? 
Jufo and also some data from Ilona (growth rate worked with that data)
* Are the relevant files linked into the raspir `work` folder ? 
yes
* Does the `raspir_fileprep` complete successfully ? See `work`
yes
* Are there enough reads in the sample for raspir ?
I think so

This is strange, because it has been working fine this side for weeks with the test fastqs from https://github.com/colindaven/ref_testing

I do not think that the data is the problem. raspir.py does not run for whatever reason (it is in the right work directory). In the .command.out there is nothing, even though I modified raspir.py to print something as soon as it is started

LisaHollstein commented 2 years ago

--> does yours look similar ? Identical ? Please export to file, and yours too, then compare with

It's similar, but not identical

LisaHollstein commented 2 years ago

I created a new haybaler conda env with the current version of env.haybaler.yml and now I get : ModuleNotFoundError: No module named 'matplotlib'

I only wonder why this isn't an issue for you, since your conda environment doesn't seem to include matplotlib as well (and also I have the newest version of the haybaler conda env)

colindaven commented 2 years ago

Ah, that could be it. It should throw an error though when you do bash runbatch_raspir.sh or python3 raspir.py in the work directory (you can get the exact command from .command.shI think.

Can you add these two to your haybaler env locally and reinstall the env ?

when in haybaler_env
mamba install matplotlib

# these are from the wochenende env but probably match the slightly different python version
  - matplotlib=3.3.4=py37h06a4308_0
  - matplotlib-base=3.3.4=py37h62a2d02_0

By the way, I have another matplotlib installed on my cluster submit machine in the below dir, which is why I wasn't seeing the problem.

ls ~/.local/lib/python3.7/site-packages/

Maybe we should go back to using the old raspir env, but it's just really annoying to have to use 3 different envs for one tool. I would vote more for combining the raspir and haybaler envs better.

Edit:

raspir needs all these python libs, scipy might be missing as well from the haybaler env

import os
import sys
import argparse
import logging
import itertools
import random
import warnings
from itertools import count, takewhile

warnings.simplefilter(action='ignore', category=Warning)

import pandas as pd
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from scipy import fftpack, stats
from scipy.stats import linregress

colindaven commented 2 years ago

Just checked, scipy should be ok, but please add the matplotlib version you get installed to

https://github.com/MHH-RCUG/haybaler/blob/dev/env.haybaler.yml

Thanks and sorry about this one ...

LisaHollstein commented 2 years ago

I have some problems with adding matplotlib to the env:

Encountered problems while solving:
  - package matplotlib-base-3.3.4-py37h62a2d02_0 requires freetype >=2.10.4,<3.0a0, but none of the providers can be installed

LisaHollstein commented 2 years ago

But running the raspir stage with the raspir conda env works, so the problem is definetly just the conda env!

colindaven commented 2 years ago

mamba install -c conda-forge matplotlib

does that pull in the freetype ?

Ok great, good to know what the problem is

LisaHollstein commented 2 years ago

mamba install -c conda-forge matplotlib does not work either


# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
        return func(*args, **kwargs)
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 898, in exception_converter
        raise e
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 892, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 851, in _wrapped_main
        result = do_call(args, p)
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 732, in do_call
        exit_code = install(args, parser, "install")
      File "/mnt/ngsnfs/gen/rcug_lw/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 590, in install
        downloaded = transaction.prompt(repos)
    RuntimeError: Found incorrect download. Aborting

`$ /mnt/ngsnfs/gen/rcug_lw/miniconda3/condabin/mamba install -c conda-forge matplotlib`

  environment variables:
     AUGUSTUS_CONFIG_PATH=/mnt/ngsnfs/tools/augustus-3.2.1/config/
      AUTOJUMP_ERROR_PATH=/home/rcug_lw/.local/share/autojump/errors.log
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=haybaler_new
                CONDA_EXE=/mnt/ngsnfs/gen/rcug_lw/miniconda3/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP=
             CONDA_PREFIX=/mnt/ngsnfs/gen/rcug_lw/miniconda3/envs/haybaler_new
    CONDA_PROMPT_MODIFIER=(haybaler_new)
         CONDA_PYTHON_EXE=/mnt/ngsnfs/gen/rcug_lw/miniconda3/bin/python
               CONDA_ROOT=/mnt/ngsnfs/gen/rcug_lw/miniconda3
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=/mnt/ngsnfs/tools/miniconda3/etc/pki/tls/certs/
       DRMAA_LIBRARY_PATH=/usr/lib/slurm-drmaa/lib/libdrmaa.so
                FTP_PROXY=<set>
              HTTPS_PROXY=<set>
               HTTP_PROXY=<set>
          LD_LIBRARY_PATH=/mnt/ngsnfs/tools/mpich-3.1.4/mpich-3.1.4/lib:/mnt/ngsnfs/tools/jemall
                          oc/lib:/mnt/ngsnfs/tools/jellyfish/lib:/mnt/ngsnfs/tools/root/root/lib
                          :/mnt/ngsnfs/tools/openmpi/openmpi-1.8.1/lib:/mnt/ngsnfs/tools/bambamc
                          /lib:/usr/lib:/mnt/ngsnfs/tools/salmon/build/lib:/usr/lib/x86_64-linux
                          -gnu/:
                     PATH=/mnt/ngsnfs/gen/rcug_lw/miniconda3/envs/haybaler_new/bin:/home/rcug_lw
                          /bin:/home/rcug_lw/.local/bin:/mnt/ngsnfs/gen/rcug_lw/miniconda3/conda
                          bin:/mnt/ngsnfs/tools/gmap/gmap-2016-09-23/bin:JRE_HOME/bin:/mnt/ngsnf
                          s/tools/nextflow:/mnt/ngsnfs/tools/drop-seq-tools/Drop-seq_tools-1.13:
                          /mnt/ngsnfs/tools/vg/vg/bin:/mnt/ngsnfs/tools/bbmap38.75:/mnt/ngsnfs/t
                          ools/SPRING/build:/mnt/ngsnfs/tools/deSALT/src:/mnt/ngsnfs/tools/bwa-
                          mem2/bwa-mem2-2.0pre1_x64-linux:/mnt/ngsnfs/tools/cellranger/cellrange
                          r-3.0.2:/mnt/ngsnfs/tools/gencore:/mnt/ngsnfs/tools/tardis/tardis:/mnt
                          /ngsnfs/tools/bamscale:/mnt/ngsnfs/tools/bigwig:/mnt/ngsnfs/tools/samt
                          ools-1.8:/mnt/ngsnfs/tools/bowtie2/bowtie2-2.4.4-linux-x86_64:/mnt/ngs
                          nfs/tools/genmap:/mnt/ngsnfs/tools/shasta:/mnt/ngsnfs/tools/slivar:#/m
                          nt/ngsnfs/tools/bcl2fastq:/mnt/ngsnfs/tools/bcl2fastq2-v2.20.0.422/bin
                          :/mnt/ngsnfs/tools/FastQC_v0.11.9:/mnt/ngsnfs/tools/tardis/mrfast:/mnt
                          /ngsnfs/tools/uxy/uxy:/mnt/ngsnfs/tools/git-lfs:/mnt/ngsnfs/tools/flap
                          pie:/mnt/ngsnfs/tools/bless/v1p02:/mnt/ngsnfs/tools/ntedit/nthits:/mnt
                          /ngsnfs/tools/ntedit/ntedit:/mnt/ngsnfs/tools/whisper:/mnt/ngsnfs/tool
                          s/duphold:/mnt/ngsnfs/tools/ra/ra/build/bin:/mnt/ngsnfs/tools/NanoVar/
                          scripts:/mnt/ngsnfs/tools/cobalt/bin:/mnt/ngsnfs/tools/biscuit:/mnt/ng
                          snfs/tools/seqkit:/mnt/ngsnfs/tools/proovread/bin:/mnt/ngsnfs/tools/ne
                          ofetch/neofetch-3.3.0:/mnt/ngsnfs/tools/flye/Flye-2.3/bin:/mnt/ngsnfs/
                          tools/spades/SPAdes-3.11.0-Linux/bin:/mnt/ngsnfs/tools/mummer4/mummer-
                          4.0.0beta2/bin/bin:/mnt/ngsnfs/tools/julia/julia-1.1.0/bin:/mnt/ngsnfs
                          /tools/fastp/fastp:/mnt/ngsnfs/tools/elPrep/elprep4:/mnt/ngsnfs/tools/
                          icgc:/mnt/ngsnfs/tools/gotop:/mnt/ngsnfs/tools/defiant/defiant:/mnt/ng
                          snfs/tools/TRF:/mnt/ngsnfs/tools/REPET/REPET_linux-x64-2.2:/mnt/ngsnfs
                          /tools/lumpy-sv/bin:/mnt/ngsnfs/tools/bayestyper/bayesTyper_v1.3.1_lin
                          ux_x86_64/bin:/mnt/ngsnfs/tools/RepeatMasker/RepeatMasker:/mnt/ngsnfs/
                          tools/RepeatModeler/RepeatScout/RepeatScout-1:/mnt/ngsnfs/tools/genome
                          tools/bin:/mnt/ngsnfs/tools/smoove:/mnt/ngsnfs/tools/RECON/RECON-1.08:
                          /mnt/ngsnfs/tools/RECON/RECON-1.08/scripts:/mnt/ngsnfs/tools/PILER:/mn
                          t/ngsnfs/tools/hercules/bin:/mnt/ngsnfs/tools/indexcov:/mnt/ngsnfs/too
                          ls/mpich-3.1.4/mpich-3.1.4/bin:/mnt/ngsnfs/tools/openmpi-1.8.1/bin:/mn
                          t/ngsnfs/tools/parallel/parallel-20141122/bin:/mnt/ngsnfs/tools/STAR/S
                          TAR_2_5_1/STAR/bin/Linux_x86_64_static:/mnt/ngsnfs/tools/cufflinks-2.2
                          .1.Linux_x86_64:/mnt/ngsnfs/tools/fastx/bin:/mnt/ngsnfs/tools/trinity/
                          trinityrnaseq-2.0.6:/mnt/ngsnfs/tools/diamond_7.9:/mnt/ngsnfs/tools/me
                          raculous/bin:/mnt/ngsnfs/tools/aragorn1.2.36:/mnt/ngsnfs/tools/tbl2asn
                          :/mnt/ngsnfs/tools/mauve_snapshot_2015-02-13/linux-x64:/mnt/ngsnfs/too
                          ls/ngsutils/ngsutils-ngsutils-0.5.7/bin:/mnt/ngsnfs/tools/malt:/mnt/ng
                          snfs/tools/mugsy_latest:/mnt/ngsnfs/tools/last/last/bin:/mnt/ngsnfs/to
                          ols/Lighter:/mnt/ngsnfs/tools/micro:#/mnt/ngsnfs/tools/blast-2.2.26/bi
                          n:/mnt/ngsnfs/tools/blast/ncbi-
                          blast-2.4.0+/bin:/mnt/ngsnfs/tools/ncbi_blast_plus/ncbi-
                          blast-2.7.1_plus/bin:/mnt/ngsnfs/tools/lastz-distrib-1.02.00/bin:/mnt/
                          ngsnfs/tools/MUMmer3.23:/mnt/ngsnfs/tools/trig/trig-1.0/bin:/mnt/ngsnf
                          s/tools/Metassembler_1.5/bin:/mnt/ngsnfs/tools/allmaps:/mnt/ngsnfs/too
                          ls/pindel:/mnt/ngsnfs/tools/trim_galore/TrimGalore:/mnt/ngsnfs/tools/R
                          /R-3.2.2/bin:/mnt/ngsnfs/tools/bcftools-1.2:/mnt/ngsnfs/tools/vcftools
                          /bin:/mnt/ngsnfs/tools/dos2unix-7.3.2:/mnt/ngsnfs/tools/cdhit:/mnt/ngs
                          nfs/tools/clustal_omega:/mnt/ngsnfs/tools/FastUniq/source:/mnt/ngsnfs/
                          tools/bamtools/bin:/mnt/ngsnfs/tools/augustus-3.2.1/bin:/mnt/ngsnfs/to
                          ols/BISMARK/Bismark:/mnt/ngsnfs/tools/cutadapt/cutadapt-1.9.1/bin:/mnt
                          /ngsnfs/tools/root/root/bin:/mnt/ngsnfs/tools/aseq/binaries/linux64:/m
                          nt/ngsnfs/tools/vt/vt:/mnt/ngsnfs/tools/snap:/mnt/ngsnfs/tools/bedtool
                          s/bedtools-2.30.0:/mnt/ngsnfs/tools/quickmerge/quickmerge/merger:/mnt/
                          ngsnfs/tools/ucsc:/mnt/ngsnfs/tools/sra-tools/sratoolkit.2.6.3-ubuntu6
                          4/bin:/mnt/ngsnfs/tools/bedops/bin:/mnt/ngsnfs/tools/smalt-0.7.6/bin:/
                          mnt/scratch/ensembl-vep/htslib:/mnt/ngsnfs/tools/fasta-36.3.8e/bin:/mn
                          t/ngsnfs/tools/fastme-2.1.5/binaries:/mnt/ngsnfs/tools/PASApipeline/bi
                          n:/mnt/ngsnfs/tools/cmake-3.7.0-rc1/bin:/mnt/ngsnfs/tools/jdk-10.0.1/b
                          in:/mnt/ngsnfs/tools/subread/subread-1.5.1-Linux-x86_64/bin:/mnt/ngsnf
                          s/tools/salmon/build/bin:/mnt/ngsnfs/tools/Slurm_tools/partitions:/mnt
                          /ngsnfs/tools/Slurm_tools/slurmreportmonth:/mnt/ngsnfs/tools/Slurm_too
                          ls/pestat:/mnt/ngsnfs/tools/Slurm_tools/showuserjobs:/home/rcug_lw/bin
                          :/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/gam
                          es:/usr/local/games:/snap/bin
               REPET_PATH=/mnt/ngsnfs/tools/REPET_linux-x64-2.2/
       REQUESTS_CA_BUNDLE=<not set>
     SINGULARITY_BINDPATH=/ngsssd1/rcug_lw,/working2/rcug_lw
            SSL_CERT_FILE=<not set>
                ftp_proxy=<set>
               http_proxy=<set>
              https_proxy=<set>
                 no_proxy=<set>

     active environment : haybaler_new
    active env location : /mnt/ngsnfs/gen/rcug_lw/miniconda3/envs/haybaler_new
            shell level : 1
       user config file : /home/rcug_lw/.condarc
 populated config files : /home/rcug_lw/.condarc
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.9.1.final.0
       virtual packages : __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /mnt/ngsnfs/gen/rcug_lw/miniconda3  (writable)
      conda av data dir : /mnt/ngsnfs/gen/rcug_lw/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /mnt/ngsnfs/gen/rcug_lw/miniconda3/pkgs
                          /home/rcug_lw/.conda/pkgs
       envs directories : /mnt/ngsnfs/gen/rcug_lw/miniconda3/envs
                          /home/rcug_lw/.conda/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.25.1 CPython/3.9.1 Linux/5.4.0-107-generic ubuntu/20.04.4 glibc/2.31
                UID:GID : 9419:9419
             netrc file : None
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

colindaven commented 2 years ago

retry, proxy server error ?

And or

mamba clean

then retry

LisaHollstein commented 2 years ago

Got the same error

colindaven commented 2 years ago

just installed successfully with a different conda channel (not conda-forge, bioconda)

mamba install -c bioconda matplotlib

colindaven commented 2 years ago

or just add - matplotlib=3.5.3 to your haybaler env and reinstall, hope one option works on your system.

MHH-RCUG / nf_wochenende

raspir error #76