'NoneType' object is not iterable

[sunliang3361]

Hello, do you know what my problem is ? Here is the log file below:

2021-04-08 14:53:19,547 NanoPlot 1.35.4 started with arguments Namespace(N50=False, alength=False, bam=None, barcoded=False, color='#4CB391', colormap='Greens', cram=None, downsample=None, dpi=100, drop_outliers=False, fasta=None, fastq=['FAO58567.fastq'], fastq_minimal=None, fastq_rich=None, feather=None, font_scale=1, hide_stats=False, huge=False, info_in_report=False, legacy=False, listcolormaps=False, listcolors=False, loglength=False, maxlength=40000, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='.', path='./', percentqual=False, pickle=None, plots=['hex', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=8, title=None, tsv_stats=False, ubam=None, verbose=False) 2021-04-08 14:53:19,548 Python version is: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20) [GCC 7.3.0] 2021-04-08 14:53:19,571 Nanoget: Starting to collect statistics from plain fastq file. 2021-04-08 15:01:40,341 Reduced DataFrame memory usage from 51.81884765625Mb to 34.5458984375Mb 2021-04-08 15:01:40,590 Nanoget: Gathered all metrics of 2264000 reads 2021-04-08 15:01:42,595 Calculated statistics 2021-04-08 15:01:42,598 Using sequenced read lengths for plotting. 2021-04-08 15:01:43,015 Hidding 930 reads longer than 40000bp in length plots. 2021-04-08 15:01:43,200 NanoPlot: Valid color #4CB391. 2021-04-08 15:01:43,201 NanoPlot: Valid colormap Greens. 2021-04-08 15:01:43,588 NanoPlot: Creating length plots for Read length. 2021-04-08 15:01:43,615 NanoPlot: Using 2263070 reads maximum of 39994bp. 2021-04-08 15:01:43,981 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:43,981 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:44,284 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:44,284 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:44,352 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:44,352 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:44,531 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:44,531 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:46,527 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:46,527 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:46,527 Created length plots 2021-04-08 15:01:46,697 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 2263070 reads. 2021-04-08 15:01:47,504 No static plots are saved due to some kaleido problem: 2021-04-08 15:01:47,504 The kaleido executable is required by the kaleido Python library, but it was not included in the Python package and it could not be found on the system PATH.

Searched for included kaleido executable at: /programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/kaleido/executable/kaleido

Searched for executable 'kaleido' on the following system PATH: /programs/x86_64-linux/nanoplot/1.35.4/bin /programs/x86_64-linux/system/biogrids_bin /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin /opt/ohpc/pub/compiler/gcc/8.3.0/bin /opt/ohpc/pub/utils/prun/1.3 /opt/ohpc/pub/utils/autotools/bin /opt/ohpc/pub/bin /usr/lib64/qt-3.3/bin /usr/local/bin /usr/bin /usr/local/sbin /usr/sbin /home/ch213537/.local/bin /home/ch213537/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin .

2021-04-08 15:01:47,504 'NoneType' object is not iterable Traceback (most recent call last): File "/programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 105, in main plots = make_plots(datadf, settings) File "/programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 174, in make_plots title=settings["title"]) TypeError: 'NoneType' object is not iterable

[wdecoster]

Thanks for reporting this. It is not immediately obvious to me what causes this error, but we will investigate.

[iliasbukraa]

@sunliang3361 a couple of questions to resolve this issue: what operating system are you using to run NanoPlot? Could you provide us with the running version of the kaleido package (pip show kaleido should do the trick). And lastly, what package manager did you use to install NanoPlot (conda/pip). Thanks!

[sunliang3361]

@iliasbukraa @wdecoster

1. We used CentOS Linux release 7.9.2009

2: $ ./python Python 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. im>>> import kaleido

print(kaleido.version) 0.1.0

3: nanoplot installed by conda: nanoplot 1.35.4 pyhdfd78af_0 bioconda

[iliasbukraa]

If I could suggest an update of the kaleido package, there have been issues with the 0.1.0 release. Could you rerun NanoPlot and see if the issues persists?

[sunliang3361]

Thank you. I have updated Kaleido package, there is no kaleido problem now but still 'NoneType' error.

2021-04-09 11:45:14,774 NanoPlot 1.35.4 started with arguments Namespace(N50=False, alength=False, bam=None, barcoded=False, color='#4CB391', colormap='Greens', cram=None, downsample=None, dpi=100, drop_outliers=False, fasta=None, fastq=['FAO58567.fastq'], fastq_minimal=None, fastq_rich=None, feather=None, font_scale=1, hide_stats=False, huge=False, info_in_report=False, legacy=False, listcolormaps=False, listcolors=False, loglength=False, maxlength=40000, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='.', path='./', percentqual=False, pickle=None, plots=['hex', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=8, title='Nanopore_Eliot', tsv_stats=False, ubam=None, verbose=False) 2021-04-09 11:45:14,774 Python version is: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20) [GCC 7.3.0] 2021-04-09 11:45:14,794 Nanoget: Starting to collect statistics from plain fastq file. 2021-04-09 11:54:38,826 Reduced DataFrame memory usage from 51.81884765625Mb to 34.5458984375Mb 2021-04-09 11:54:39,012 Nanoget: Gathered all metrics of 2264000 reads 2021-04-09 11:54:40,771 Calculated statistics 2021-04-09 11:54:40,773 Using sequenced read lengths for plotting. 2021-04-09 11:54:41,109 Hidding 930 reads longer than 40000bp in length plots. 2021-04-09 11:54:41,226 NanoPlot: Valid color #4CB391. 2021-04-09 11:54:41,227 NanoPlot: Valid colormap Greens. 2021-04-09 11:54:41,430 NanoPlot: Creating length plots for Read length. 2021-04-09 11:54:41,446 NanoPlot: Using 2263070 reads maximum of 39994bp. 2021-04-09 11:54:53,930 Created length plots 2021-04-09 11:54:54,134 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 2263070 reads. 2021-04-09 11:54:57,089 'NoneType' object is not iterable Traceback (most recent call last): File "/programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 105, in main plots = make_plots(datadf, settings) File "/programs/x86_64-linux/nanoplot/1.35.4/nanoplot_extlib/miniconda3-2019.07-sck6/lib/python3.7/site-packages/nanoplot/NanoPlot.py", line 174, in make_plots title=settings["title"]) TypeError: 'NoneType' object is not iterable

[wdecoster]

Thanks for the update, I think I identified the issue and will provide a fix later tonight.

[wdecoster]

Thanks for your patience, the issue should be solved in NanoPlot v1.35.5.

Cheers, Wouter