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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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NanoPlot Report Not Containing any Plot #253

Closed ursadhip closed 3 years ago

ursadhip commented 3 years ago

Command used: $ nanoplot -t 4 --fastq ./demultiplex_nc_qcat_NBD104_adaptrim_porechop_16_11_2020/barcode01_ad_trm.fastq -o ./nanoplot Problem: Nanoplot reports html file is not containing only the summary statistics, no plot. All other generated HTML files of plots are also empty.

wdecoster commented 3 years ago

Could you please share the log file?

ursadhip commented 3 years ago

PFA the log file for your reference.

On Wed, Apr 14, 2021 at 5:06 PM Wouter De Coster @.***> wrote:

Could you please share the log file?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-819450460, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UVUES7HMBR5XVKGKK3TIV44NANCNFSM425FH72Q .

-- Adhip Mukhopadhyay

ursadhip commented 3 years ago

2021-04-14 12:18:41,741 NanoPlot 1.35.5 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=['./demultiplex_nc_qcat_NBD104_adaptrim_porechop_16_11_2020/barcode01_ad_trm.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=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='./nanoplot', path='./nanoplot/', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=4, title=None, tsv_stats=False, ubam=None, verbose=False) 2021-04-14 12:18:41,768 Python version is: 3.7.8 | packaged by conda-forge | (default, Jul 31 2020, 02:37:09) [Clang 10.0.1 ] 2021-04-14 12:18:42,517 Nanoget: Starting to collect statistics from plain fastq file. 2021-04-14 12:18:58,586 Reduced DataFrame memory usage from 0.9224853515625Mb to 0.614990234375Mb 2021-04-14 12:18:58,626 Nanoget: Gathered all metrics of 40304 reads 2021-04-14 12:18:58,742 Calculated statistics 2021-04-14 12:18:58,743 Using sequenced read lengths for plotting. 2021-04-14 12:18:58,796 NanoPlot: Valid color #4CB391. 2021-04-14 12:18:58,796 NanoPlot: Valid colormap Greens. 2021-04-14 12:18:58,970 NanoPlot: Creating length plots for Read length. 2021-04-14 12:18:58,994 NanoPlot: Using 40304 reads maximum of 43848bp. 2021-04-14 12:20:13,779 Created length plots 2021-04-14 12:20:13,798 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 40304 reads. 2021-04-14 12:20:23,859 Created LengthvsQual plot 2021-04-14 12:20:23,883 Writing html report. 2021-04-14 12:20:24,292 Finished!

sulheim commented 3 years ago

Which browser do yoou use @ursadhip? My html-reports only render properly in Firefox, not in Edge or Chrome (possibly very slow).

wdecoster commented 3 years ago

Do you have any thoughts about this @iliasbukraa ?

iliasbukraa commented 3 years ago

@ursadhip could you perhaps share the NanoPlot-report.html file with me? If I understand correctly, the plots are generated but they are empty? From your log file I see nothing is actually going wrong with creating the plots and html report, maybe I'll have more insight when I take a look at the report.

iliasbukraa commented 3 years ago

Which browser do yoou use @ursadhip? My html-reports only render properly in Firefox, not in Edge or Chrome (possibly very slow).

@sulheim may I ask what you mean with render properly? Are figures not showing or? I have tried opening NanoPlot-report.html with Firefox, Chrome and Opera and no issues there. Thanks!

ursadhip commented 3 years ago

Sure I will check as per your suggestion, and let you know by sharing the NanoPlot-report.html.

On Thu, Apr 15, 2021 at 5:06 PM iliasbukraa @.***> wrote:

Which browser do yoou use @ursadhip https://github.com/ursadhip? My html-reports only render properly in Firefox, not in Edge or Chrome (possibly very slow).

may I ask what you mean with render properly? Are figures not showing or? I have tried opening NanoPlot-report.html with Firefox, Chrome and Opera and no issues there. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-820355015, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UQIUA5XNQJJJY43CG3TI3FVBANCNFSM425FH72Q .

-- Adhip Mukhopadhyay

ursadhip commented 3 years ago

Yeah, you were right. The file is opening on the Safari browser, not in Chrome. But there is some minor issue with the Plot title "LengthvsQualityScatterPlot_kde" and its scale in X-axis where 40K is overlapping with 0. The same is true for the .png of the same. Please have the NanoPlot-report.html and LengthvsQualityScatterPlot_kde.png for your reference.

On Thu, Apr 15, 2021 at 9:54 PM Adhip Mukhopadhyay @.***> wrote:

Sure I will check as per your suggestion, and let you know by sharing the NanoPlot-report.html.

On Thu, Apr 15, 2021 at 5:06 PM iliasbukraa @.***> wrote:

Which browser do yoou use @ursadhip https://github.com/ursadhip? My html-reports only render properly in Firefox, not in Edge or Chrome (possibly very slow).

may I ask what you mean with render properly? Are figures not showing or? I have tried opening NanoPlot-report.html with Firefox, Chrome and Opera and no issues there. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-820355015, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UQIUA5XNQJJJY43CG3TI3FVBANCNFSM425FH72Q .

-- Adhip Mukhopadhyay

-- Adhip Mukhopadhyay

iliasbukraa commented 3 years ago

@ursadhip if the plots are not opening in your web browser, maybe your web browser is blocking the execution of JS? If the NanoPlot-report.html opens in the same web browser on another pc, that will be the problem then.

I'm not sure what the issue is with the overlapping title and x-axis since you haven't shared the .png or .html, but I suspect it has something to do with how the web browser (safari) handles the JS in the plots. I'd still like to take a look at the .png/.html to see what the issue is 👍

sulheim commented 3 years ago

Which browser do yoou use @ursadhip? My html-reports only render properly in Firefox, not in Edge or Chrome (possibly very slow).

@sulheim may I ask what you mean with render properly? Are figures not showing or? I have tried opening NanoPlot-report.html with Firefox, Chrome and Opera and no issues there. Thanks!

@iliasbukraa after investigating this further I think the issue was actually my firewall. Switching network resolved my issue with rendering the html report properly. I believe it might be a cache-thing that made me believe that it only worked with firefox.

ursadhip commented 3 years ago

Have a look on the X-axis in the '.png'

On Sat, Apr 17, 2021 at 6:17 PM iliasbukraa @.***> wrote:

@ursadhip https://github.com/ursadhip if the plots are not opening in your web browser, maybe your web browser is blocking the execution of JS? If the NanoPlot-report.html opens in the same web browser on another pc, that will be the problem then.

I'm not sure what the issue is with the overlapping title and x-axis since you haven't shared the .png or .html, but I suspect it has something to do with how the web browser (safari) handles the JS in the plots. I'd still like to take a look at the .png/.html to see what the issue is 👍

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-821817397, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UWNDUKS76SCTTNO7S3TJF7MJANCNFSM425FH72Q .

-- Adhip Mukhopadhyay

iliasbukraa commented 3 years ago

@ursadhip this should now be fixed, I added a 45 degree angle to the x-axis so there is no overlap.

ursadhip commented 3 years ago

Ok but what about the very same plot title? Is was also not completely appearing. Please check and let me know.

On Tue 20 Apr, 2021, 11:29 PM iliasbukraa, @.***> wrote:

@ursadhip https://github.com/ursadhip this should now be fixed, I added a 45 degree angle to de x-axis so there is no overlap.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-823485660, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UTTZQ7DTJI3L6DT3ATTJW6HRANCNFSM425FH72Q .

wdecoster commented 3 years ago

Please check and let me know.

Hey, that's not how this works. We are open source software developers, and we are happy to help where we can and when we can. This is often in our free time.

If you don't make the effort to show us an image of what you are talking about, then don't expect us to quickly solve your problems. We would like to make NanoPlot useful and nice for everyone, but we are not just sitting at our computer waiting for users to open issues. You are not a customer.

Regards, Wouter

RamRS commented 3 years ago

@ursadhip I understand that your statement might be owing to a language barrier, but "please check and let me know" doesn't translate well as a phrase in English. You should state your problem/requirement and leave it at that. In this case, just say that the plot title does not appear completely. Stating what the developer should do about it (unless you're making a different version of that statement in the form of constructive criticism) is rude.

ursadhip commented 3 years ago

My sincere apology.

Actually, I am new to this GitHub world and have deep respect for this community for their effort. So, no offense, please.

@RamRS Yes, hopefully, it's a language issue, I wasn't able to convey my problem in well, manner. So thanks for the suggestion.

On Wed 21 Apr, 2021, 9:01 PM Ram Srinivasan, @.***> wrote:

@ursadhip https://github.com/ursadhip I understand that your statement might be owing to a language barrier, but "please check and let me know" doesn't translate well as a phrase in English. You should state your problem/requirement and leave it at that. In this case, just say that the plot title does not appear completely. Stating what the developer should do about it (unless you're making a different version of that statement in the form of constructive criticism) is rude.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wdecoster/NanoPlot/issues/253#issuecomment-824155415, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ2T5UVFG243AGFB2W5D7BDTJ3VU3ANCNFSM425FH72Q .

wdecoster commented 3 years ago

I think we should have some changes ready soon which may improve on the problem you see, but if you could post examples that would always be helpful.

wdecoster commented 3 years ago

This should be improved in NanoPlot v1.36.0, available through pip and probably soon through conda. Please let us know if you see another issue.