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Kinggerm / GetOrganelle

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
GNU General Public License v3.0
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Running getorg with unpaired reads #143

Closed passelma42 closed 2 years ago

passelma42 commented 2 years ago

Hi,

I'm trying to run Getorg with unpaired reads. Previous runs with PE reads are not a problem. Here an overview of my commands and terminal output. Could you please point me in the right direction? Thanks!

vsc43352@node3507:~/scratch_vo/getorg/TLP/getorg_testrun$get_organelle_from_reads.py -u ./TLP1218_R1_trimmed.fq -o ./TLP1218_getorg_out -R 25 -k 21,45,65,85,105 -F embplant_pt

GetOrganelle v1.7.4-pre2

get_organelle_from_reads.py assembles organelle genomes from genome skimming data. Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.6 (default, Feb 24 2021, 09:52:39) [GCC 10.2.0] PLATFORM: Linux node3507.doduo.os 4.18.0-305.34.2.el8_4.x86_64 #1 SMP Mon Jan 17 09:42:23 EST 2022 x86_64 x86_64 PYTHON LIBS: GetOrganelleLib 1.7.4-pre2; numpy 1.19.4; sympy 1.7.1; scipy 1.5.4; psutil 5.7.2 DEPENDENCIES: Bowtie2 2.4.2; SPAdes genome assembler 3.15.2; Blast 2.11.0; Bandage 0.8.1 GETORG_PATH=/user/gent/433/vsc43352/.GetOrganelle SEED DB: embplant_pt 0.0.1; embplant_mt 0.0.1 LABEL DB: embplant_pt 0.0.1; embplant_mt 0.0.1 WORKING DIR: /kyukon/scratch/gent/vo/001/gvo00142/vsc43352/getorg/TLP/getorg_testrun /apps/gent/RHEL8/haswell-ib/software/GetOrganelle/1.7.4-pre2-foss-2020b/bin/get_organelle_from_reads.py -u ./TLP1218_R1_trimmed.fq -o ./TLP1218_getorg_out -R 25 -k 21,45,65,85,105 -F embplant_pt

Traceback (most recent call last): File "/apps/gent/RHEL8/haswell-ib/software/GetOrganelle/1.7.4-pre2-foss-2020b/bin/get_organelle_from_reads.py", line 4136, in main() File "/apps/gent/RHEL8/haswell-ib/software/GetOrganelle/1.7.4-pre2-foss-2020b/bin/get_organelle_from_reads.py", line 3713, in main get_options(description=title, version=get_versions()) File "/apps/gent/RHEL8/haswell-ib/software/GetOrganelle/1.7.4-pre2-foss-2020b/bin/get_organelle_from_reads.py", line 683, in get_options assert is_valid_path(os.path.basename(fq_file)), \ File "/apps/gent/RHEL8/haswell-ib/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/posixpath.py", line 142, in basename p = os.fspath(p) TypeError: expected str, bytes or os.PathLike object, not NoneType

And here an overview of the loaded modules on our cluster: Currently Loaded Modules: 1) cluster/slaking (S) 21) bzip2/1.0.8-GCCcore-10.2.0 41) libpng/1.6.37-GCCcore-10.2.0 2) GCCcore/10.2.0 22) ncurses/6.2-GCCcore-10.2.0 42) NASM/2.15.05-GCCcore-10.2.0 3) zlib/1.2.11-GCCcore-10.2.0 23) libreadline/8.0-GCCcore-10.2.0 43) libjpeg-turbo/2.0.5-GCCcore-10.2.0 4) binutils/2.35-GCCcore-10.2.0 24) Tcl/8.6.10-GCCcore-10.2.0 44) LMDB/0.9.24-GCCcore-10.2.0 5) GCC/10.2.0 25) SQLite/3.33.0-GCCcore-10.2.0 45) BLAST+/2.11.0-gompi-2020b 6) numactl/2.0.13-GCCcore-10.2.0 26) GMP/6.2.0-GCCcore-10.2.0 46) expat/2.2.9-GCCcore-10.2.0 7) XZ/5.2.5-GCCcore-10.2.0 27) libffi/3.3-GCCcore-10.2.0 47) DB/18.1.40-GCCcore-10.2.0 8) libxml2/2.9.10-GCCcore-10.2.0 28) Python/3.8.6-GCCcore-10.2.0 48) Perl/5.32.0-GCCcore-10.2.0 9) libpciaccess/0.16-GCCcore-10.2.0 29) Bandage/0.8.1_Centos 49) freetype/2.10.3-GCCcore-10.2.0 10) hwloc/2.2.0-GCCcore-10.2.0 30) pybind11/2.6.0-GCCcore-10.2.0 50) util-linux/2.36-GCCcore-10.2.0 11) libevent/2.1.12-GCCcore-10.2.0 31) SciPy-bundle/2020.11-foss-2020b 51) fontconfig/2.13.92-GCCcore-10.2.0 12) UCX/1.9.0-GCCcore-10.2.0 32) MPFR/4.1.0-GCCcore-10.2.0 52) xorg-macros/1.19.2-GCCcore-10.2.0 13) libfabric/1.11.0-GCCcore-10.2.0 33) MPC/1.2.1-GCCcore-10.2.0 53) X11/20201008-GCCcore-10.2.0 14) PMIx/3.1.5-GCCcore-10.2.0 34) gmpy2/2.1.0b5-GCC-10.2.0 54) Tk/8.6.10-GCCcore-10.2.0 15) OpenMPI/4.0.5-GCC-10.2.0 35) sympy/1.7.1-foss-2020b 55) Tkinter/3.8.6-GCCcore-10.2.0 16) OpenBLAS/0.3.12-GCC-10.2.0 36) SPAdes/3.15.2-GCC-10.2.0 56) LibTIFF/4.1.0-GCCcore-10.2.0 17) gompi/2020b 37) tbb/2020.3-GCCcore-10.2.0 57) Pillow/8.0.1-GCCcore-10.2.0 18) FFTW/3.3.8-gompi-2020b 38) Bowtie2/2.4.2-GCC-10.2.0 58) matplotlib/3.3.3-foss-2020b 19) ScaLAPACK/2.1.0-gompi-2020b 39) PCRE/8.44-GCCcore-10.2.0 59) GetOrganelle/1.7.4-pre2-foss-2020b

Kinggerm commented 2 years ago

The current version is a pre-release version one year ago. I believe you can solve the ERROR by updating GetOrganelle, preferably to the latest version.

Please let me know your updates.