FileNotFoundError at /srnade/result webserver - local sRNAde run blocks

[klaasdewaele]

Hello,

Thanks for creating such a useful tool! I greatly appreciate it since it has made many of my miRNA analyses easier and robuster.

However, currently I'm experiencing trouble using sRNAtoolbox for miRNA differential expression analysis, both with a local installation and with the webserver version.

On the webservice, I tried to launch my finished sRNAbench run (0MQXTITET1Y7B7S) with sRNAde. However, repeatedly, it aborts with the following error:

<h1>FileNotFoundError at /srnade/result</h1>
  <pre class="exception_value">[Errno 2] No such file or directory: 'de/ttest'</pre>

Request Method: | GET
-- | --
http://localhost:8012/srnatoolbox/srnade/result?id=ENOPD3OA4V83H5T
1.11.2
FileNotFoundError
[Errno 2] No such file or directory: 'de/ttest'
/opt/sRNAtoolbox_prod/sRNAtoolboxweb/sRNAde/views.py in find_matrix_URL, line 319
/opt/venv/sRNAtoolbox2019/bin/python
3.5.2
['/opt/sRNAtoolbox_prod/sRNAtoolboxweb',  '/usr/lib/python35.zip',  '/usr/lib/python3.5',  '/usr/lib/python3.5/plat-x86_64-linux-gnu',  '/usr/lib/python3.5/lib-dynload',  '/opt/venv/sRNAtoolbox2019/lib/python3.5/site-packages',  '/opt/venv/sRNAtoolbox2019/lib/python3.5/site-packages/IPython/extensions']
Sat, 22 Jul 2023 15:19:44 +0000

I am uncertain whether this is a problem on the webserver pipeline's side?

Regarding my local installation of sRNAtoolbox (for use with a nonmodel protozoic species), sRNAde doesn't advance beyond the 'microRNA analysis' stage, no matter how long the script runs (see log below). I'm on a Linux Ubuntu 18.04.3 with 32 GB RAM and eight 2.2 GHz CPUs, which are sufficient resources I suppose?

I use LaunchDE with the following command (and a custom samplesheet.tsv):

sudo /srv/bin/LaunchDE /shared/shared_folder/samplesheet.tsv /shared/shared_folder/final_srnatoolbox_out_srnade/ /shared/shared_folder/srnade_out

The output (sub)folders are generated, but none of the output files contain any output:

Stdout:

srna@sRNAtoolbox:/shared/shared_folder/srnade_out$ sudo /srv/bin/LaunchDE /shared/shared_folder/samplesheet.tsv /shared/shared_folder/final_srnatoolbox_out_srnade/ /shared/shared_folder/srnade_out

             Using the default database path
             Detected tab as separator in sample sheet file!
             Start with differential expression of microRNAs
             Start with genomeDistribution (if exists)
             Start with mapping statistics
             Start with read length
             Start with isoMiR analysis (if isoMiR data exists)
             Start with microRNA analysis at a read level (each annotated microRNA)
             Start with microRNA analysis (no minimum read count)

The logFile.txt doesn't report any errors:

2023-07-22 17:47:39.247 INFO: Generating expression matrixes.
2023-07-22 17:47:39.331 INFO: Launch differential expression for: /shared/shared_folder/srnade_out
2023-07-22 17:47:39.333 INFO: /opt/local/R-3.5.3/bin/Rscript /opt/sRNAtoolboxDB/r/de_deseq2.R /shared/shared_folder/srnade_out//mature_sense_minExpr0_RCadj.mat m,m,m,m,m,g_pos,g_pos,g_pos,g_pos,g_pos,g_pos,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_pos /shared/shared_folder/srnade_out/de_deseq2 mature_sense_minExpr0_RCadj 0.05 
2023-07-22 17:47:47.521 INFO: /opt/local/R-3.5.3/bin/Rscript /opt/sRNAtoolboxDB/r/de_deseq.R /shared/shared_folder/srnade_out//mature_sense_minExpr0_RCadj.mat m,m,m,m,m,g_pos,g_pos,g_pos,g_pos,g_pos,g_pos,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_pos /shared/shared_folder/srnade_out/de_deseq mature_sense_minExpr0_RCadj 0.05 
2023-07-22 17:47:52.715 INFO: /opt/local/R-3.5.3/bin/Rscript /opt/sRNAtoolboxDB/r/de_edger.R /shared/shared_folder/srnade_out//mature_sense_minExpr0_RCadj.mat m,m,m,m,m,g_pos,g_pos,g_pos,g_pos,g_pos,g_pos,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_pos /shared/shared_folder/srnade_out/de_edger mature_sense_minExpr0_RCadj 0.05 
2023-07-22 17:47:53.269 INFO: /opt/local/R-3.5.3/bin/Rscript /opt/sRNAtoolboxDB/r/de_noiseq.R /shared/shared_folder/srnade_out//mature_sense_minExpr0_RCadj.mat m,m,m,m,m,g_pos,g_pos,g_pos,g_pos,g_pos,g_pos,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,g_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_neg,s_pos /shared/shared_folder/srnade_out/de_noiseq mature_sense_minExpr0_RCadj 0.05 

Many thanks for any directions on how to troubleshoot this!

[tkasuga]

Same here. I tried several different combinations of my samples but always get the same error: FileNotFoundError at /srnade/result [Errno 2] No such file or directory: 'de/ttest'

[ThiemoMMoellenkamp]

ah, I have just opened an issue myself, but it's the same problem.

[slavictoast]

Hey you all, what helped in my case was selecting the group string section (see picture with red rectangle) and retrying the sRNAde pipeline. I don't necessarily know why this fixed or rather evade the FileNotFoundError in the pipeline but maybe it works for you too!

[ThiemoMMoellenkamp]

Hi, thanks for the suggestion - I tried it, and for me it resulted in the same error. So I can't seem to find the quick fix that worked for you. Sadly the support here seems not to be very active...