Error plotting plots number 4

[Jose-LSP]

Hi, I've been trying findZX with several species, with the first one it worked great, it's really wonderful the pipeline, but the next species are giving me errors plotting the number 4s. The errors are: Job 114: Plotting results 4_sexDifferences

Activating conda environment: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 Activating conda environment: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 [Tue Aug 27 09:37:08 2024] Error in rule plotting: jobid: 114 output: results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.1000000bp.pdf, results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.1000000bp.highlight.pdf, results/Halichondria_panicea/output/no_synteny/plots/.misc/plotting.1000000bp.done, results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.1000000bp.window.tsv log: results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.1000000.log (check log file(s) for error message) conda-env: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 shell:

        Rscript workflow/scripts/plot_windows.R results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.0.1000000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.2.1000000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.unfiltered.1000000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffHeterozygosity.1000000bp.out results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.1000000bp.pdf None results/Halichondria_panicea/output/no_synteny/highlight_file.list 0.0 0.2 unfiltered 1000000 results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.1000000bp.window.tsv 2> results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.1000000.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs. Select jobs to execute... [Tue Aug 27 09:37:08 2024]

Error in rule plotting: jobid: 112 [Tue Aug 27 09:37:08 2024] output: results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.100000bp.pdf, results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.100000bp.highlight.pdf, results/Halichondria_panicea/output/no_synteny/plots/.misc/plotting.100000bp.done, results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.100000bp.window.tsv Job 110: Plotting results 4_sexDifferences log: results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.100000.log (check log file(s) for error message)

Activating conda environment: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 conda-env: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 shell:

        Rscript workflow/scripts/plot_windows.R results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.0.100000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.2.100000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.unfiltered.100000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffHeterozygosity.100000bp.out results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.100000bp.pdf None results/Halichondria_panicea/output/no_synteny/highlight_file.list 0.0 0.2 unfiltered 100000 results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.100000bp.window.tsv 2> results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.100000.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs. Select jobs to execute...

[Tue Aug 27 09:37:08 2024] Job 113: Plotting results 4_sexDifferences

Activating conda environment: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 [Tue Aug 27 09:37:10 2024] Error in rule plotting: jobid: 113 output: results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.500000bp.pdf, results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.500000bp.highlight.pdf, results/Halichondria_panicea/output/no_synteny/plots/.misc/plotting.500000bp.done, results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.500000bp.window.tsv log: results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.500000.log (check log file(s) for error message) conda-env: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 shell:

        Rscript workflow/scripts/plot_windows.R results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.0.500000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.2.500000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.unfiltered.500000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffHeterozygosity.500000bp.out results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.500000bp.pdf None results/Halichondria_panicea/output/no_synteny/highlight_file.list 0.0 0.2 unfiltered 500000 results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.500000bp.window.tsv 2> results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.500000.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs. [Tue Aug 27 09:37:10 2024] Error in rule plotting: jobid: 110 output: results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.50000bp.pdf, results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.50000bp.highlight.pdf, results/Halichondria_panicea/output/no_synteny/plots/.misc/plotting.50000bp.done, results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.50000bp.window.tsv log: results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.50000.log (check log file(s) for error message) conda-env: /home/jose/FindZX/Hapan/.snakemake/conda/9bb2cc555575649816342a28d8507f34 shell:

        Rscript workflow/scripts/plot_windows.R results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.0.50000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.0.2.50000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffGenomeCoverage.mismatch.unfiltered.50000bp.out results/Halichondria_panicea/output/no_synteny/tables/diffHeterozygosity.50000bp.out results/Halichondria_panicea/output/no_synteny/plots/4_sexDifferences.50000bp.pdf None results/Halichondria_panicea/output/no_synteny/highlight_file.list 0.0 0.2 unfiltered 50000 results/Halichondria_panicea/output/no_synteny/tables/sexDifferences_mean_SD.50000bp.window.tsv 2> results/Halichondria_panicea/logs/plotting/no_synteny/4_sexDifferences.mismatch.50000.log

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs. Exiting because a job execution failed. Look above for error message

The only tables I can't find are the "sexDifferences_mean_SD.xxxxbp.windows.tsv"

The logs are:

Attaching package: ‘dplyr’

The following objects are masked from ‘package:plyr’:

arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize

The following objects are masked from ‘package:data.table’:

between, first, last

The following object is masked from ‘package:doBy’:

order_by

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Attaching package: ‘ggpubr’

The following object is masked from ‘package:plyr’:

mutate

The following object is masked from ‘package:cowplot’:

get_legend

Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table

Is it failing something in the previous steps?

Thank you!

[hsigeman]

Hi Jose!

Thank you, it's really nice to hear that the pipeline is useful to you.

This error can arise if the window sizes (default: 50kb, 100kb, and 1Mb) are too large for the reference genome. Is this genome more fragmented compared to the species you have analyzed previously?

If it is a very fragmented genome, you can either change the window sizes in the config file (the window_sizes parameter) and run the pipeline again, or use a reference genome with higher contiguity as a synteny-species.

Hope this helps, but let me know if it doesn't and I'll look into it further.

Good luck! Hanna

[Jose-LSP]

Hi Hanna, thank you very much. The genomes are all chromosome level, but this one has some small unplaced scaffolds, so i'll check that and the minimum scaffold size. Thank you again!