Error in makeReport step

[SegoleneDiry]

Hello,

I performed a successfull run on test_data but when I tested the workflow on my data, it gave this error :

Error executing process > 'pipeline:makeReport'

Caused by:
  Process `pipeline:makeReport` terminated with an error exit status (1)

  […]
BokehUserWarning: ColumnDataSource's columns must be of the same length. Current lengths: ('top', 2), ('x', 3)

Could you please help me ? Thanks,

[nrhorner]

Hello,

I'm sorry that you are having problems with the workflow. Could you please try the latest version (v0.1.1). And please let me know if that doesn't fix your issue.

Neil

[SegoleneDiry]

Hello, indeed, my version is v0.1.0 But I use conda and it seems that v0.1.1 is not available yet. Did I miss something?

[nrhorner]

Hi, please try nextflow pull epi2me-labs/wf-isoforms as described here before running

[SegoleneDiry]

Thanks for your answer.
After nextflow pull, I re-tried to run the workflow and I get this error :

  Traceback (most recent call last):
    File "/home/sdiry/.nextflow/assets/epi2me-labs/wf-isoforms/bin/report.py", line 901, in <module>
      main()
    File "/home/sdiry/.nextflow/assets/epi2me-labs/wf-isoforms/bin/report.py", line 866, in main
      df_tmaps = gff_compare_plots(
    File "/home/sdiry/.nextflow/assets/epi2me-labs/wf-isoforms/bin/report.py", line 374, in gff_compare_plots
      bar_performance = grouped_bar(stats, title="Performance",
    File "/home/sdiry/.nextflow/assets/epi2me-labs/wf-isoforms/bin/report.py", line 283, in grouped_bar
      max_ = df.to_numpy().max()
    File "/home/sdiry/epi2melabs_wf_isoforms/workspace_dir/conda/epi2melabs-wf-isoforms-7d2573abb6ef506fbc61e109fcbeb065/lipython3.8/site-packages/numpy/core/_methods.py", line 40, in _amax
      return umr_maximum(a, axis, None, out, keepdims, initial, where)
  ValueError: zero-size array to reduction operation maximum which has no identity

I use gff from refseq GRCh38 and I perform the run on a single fastq just for test. Could you help me please?

[nrhorner]

Hi,

Would it be possible to post the contents of str_merged.stats ? It should be somewhere like 'out_dir/sample_id/*gff_compare'

[SegoleneDiry]

Here is the contents of str_merged.stats :

$ cat mysample/str_merged.stats
# gffcompare v0.11.2 | Command line was:
#gffcompare -o mysample/str_merged -r ref.gff -R transcripts_mysample.gff
#

#= Summary for dataset: transcripts_mysample.gff
#     Query mRNAs :    2442 in    2378 loci  (2162 multi-exon transcripts)
#            (62 multi-transcript loci, ~1.0 transcripts per locus)
# Reference mRNAs :       0 in       0 loci  (0 multi-exon)

 Total union super-loci across all input datasets: 2378
2442 out of 2442 consensus transcripts written in mysample_gffcompare/str_merged.annotated.gtf (0 discarded as redundant)

[nrhorner]

gffcomapre cannot find any reference transcripts.

Can you confirm that the gff annotation file matches the genome assembly file? The first column of the gff file should match ids in the assembly file.

[SegoleneDiry]

You are right, my gff didn't match the genome assembly file. When I choose the right gff, it works well!
Thanks for your help!

[nrhorner]

No problem.