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harry-thorpe / piggy

Pipeline for analysing intergenic regions in bacteria
GNU General Public License v3.0
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failed to create IGR cluster files #26

Open Bre-Na opened 4 years ago

Bre-Na commented 4 years ago

Hi, I am trying to run Piggy for a couple of closely related bacterial genomes but the analysis fails during creation of the cluster files with “Cannot open output file: piggy/cluster_intergenic_files/Cluster_299.fasta”. However, if I check the “cluster_intergenic_files” folder it contains 2791 cluster files. (and Cluster_299.fasta can be opened) If I rerun the analysis it will fail at a different file. With the provided example data the analysis completes. Any ideas what I am doing wrong? Thanks in advance for your help!

The assemblies have been annotated with prokka (1.13.7). Roary (3.12.0) was run with “ roary -e -n -s -i 90 -z -p 8 -r ../prokka/gff/ ” Piggy (1.5) was run with “ piggy --in_dir prokka/gff/ --out_dir piggy/ --roary_dir roary/ “ Error message:

41/41 gff files processed Clustering IGRs with cd-hit... IGRs clustered Creating IGR cluster files. 1000 representative IGR cluster files created. 2000 representative IGR cluster files created. 1000 IGR cluster files created. 2000 IGR cluster files created. Cannot open output file: piggy/cluster_intergenic_files/Cluster_299.fasta failed to create IGR cluster files

harry-thorpe commented 4 years ago

Hi, I'm not sure what's causing this. How much free disk space is there? How many genomes are you analysing?

Bre-Na commented 4 years ago

Hi, Thank you for having a look at my issue. We have about 1T free disc space and I am trying to analyse 41 genomes.

I generated a fresh conda environment, installed roary and piggy. I also tried with fewer (5) samples but the error remains.

            “Cannot open output file: piggy_200303/cluster_intergenic_files/Cluster_1200.fasta

failed to create IGR cluster files”

Do you have any ideas what I could try? A different Prokka version?

Kind regards

Von: harry-thorpe notifications@github.com Gesendet: Dienstag, 3. März 2020 11:22 An: harry-thorpe/piggy piggy@noreply.github.com Cc: Bretschneider, Nancy, Dr. (LGL) Nancy.Bretschneider@lgl.bayern.de; Author author@noreply.github.com Betreff: Re: [harry-thorpe/piggy] failed to create IGR cluster files (#26)

Hi, I'm not sure what's causing this. How much free disk space is there? How many genomes are you analysing?

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harry-thorpe commented 4 years ago

That is weird. If you are able to share your data I can try it?

Bre-Na commented 4 years ago

I cant share the data. And in the mean time I figured out that the error isn’t caused by the data. I have installed piggy on a different computer and there it works perfectly with all 41 genomes. However, in the long run, I need it to run on the “first” computer so I will try to find out why it doesn’t work there (even after a new installation). If you have any ideas where to start that would be great.

Von: harry-thorpe notifications@github.com Gesendet: Dienstag, 3. März 2020 12:48 An: harry-thorpe/piggy piggy@noreply.github.com Cc: Bretschneider, Nancy, Dr. (LGL) Nancy.Bretschneider@lgl.bayern.de; Author author@noreply.github.com Betreff: Re: [harry-thorpe/piggy] failed to create IGR cluster files (#26)

That is weird. If you are able to share your data I can try it?

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