Error when using exon file about leafcutter HOT 19 CLOSED

from leafcutter.

Thank you Yang, I didn't copy the full path in my comment, but the path I am using exists (~/leafcutter/leafcutter/data/gencode19_exons.txt.gz)
Let me know if you would like any additional information!

from leafcutter.

from leafcutter.

Thank you, I used the full path and still have the same error.
Best,
Ascia

from leafcutter.

from leafcutter.

I am running this command for the example data:
/home/aeskin/leafcutter/scripts/leafcutter_ds.R -e /home/aeskin/leafcutter/leafcutter/data/gencode19_exons.txt.gz /home/aeskin/leafcutter/example_data/testYRIvsEU_perind_numers.counts.gz /home/aeskin/leafcutter/example_data/test_diff_intron.txt

/home/aeskin/leafcutter/leafcutter/data/gencode19_exons.txt.gz
chr start end strand gene_name
chr1 11869 12227 + DDX11L1
chr1 12613 12721 + DDX11L1
chr1 13221 14409 + DDX11L1
chr1 11872 12227 + DDX11L1

/home/aeskin/leafcutter/example_data/testYRIvsEU_perind_numers.counts.gz
RNA.NA06986_CEU.chr1.bam RNA.NA06994_CEU.chr1.bam RNA.NA18486_YRI.chr1.bam RNA.NA06985_CEU.chr1.bam RNA.NA18487_YRI.chr1.bam RNA.NA06989_CEU.chr1.bam RNA.NA06984_CEU.chr1.bam RNA.NA18488_YRI.chr1.bam RNA.NA18489_YRI.chr1.bam RNA.NA18498_YRI.chr1.bam
chr1:17055:17233:clu_1 21 13 18 20 17 12 11 8 15 25
chr1:17055:17606:clu_1 4 11 12 7 2 0 5 2 4 4
chr1:17368:17606:clu_1 127 132 128 55 93 90 68 43 112 137

/home/aeskin/leafcutter/example_data/test_diff_intron.txt
RNA.NA18486_YRI.chr1.bam YRI
RNA.NA18487_YRI.chr1.bam YRI
RNA.NA18488_YRI.chr1.bam YRI
RNA.NA18489_YRI.chr1.bam YRI
RNA.NA18498_YRI.chr1.bam YRI
RNA.NA06984_CEU.chr1.bam CEU
RNA.NA06985_CEU.chr1.bam CEU
RNA.NA06986_CEU.chr1.bam CEU
RNA.NA06989_CEU.chr1.bam CEU
RNA.NA06994_CEU.chr1.bam CEU

gives me:
Running differential splicing analysis...
Differential splicing summary:
statuses Freq
1 Success 523
2 <=1 sample with coverage>min_coverage 7
3 Not enough valid samples 71
4 <2 introns used in >=min_samples_per_intron samples 1
Saving results...
Loading exons from /home/aeskin/leafcutter/leafcutter/data/gencode19_exons.txt.gz
Error in try({ :
unused argument (error = function(err) warning(as.character(err)))
Execution halted

Thanks!

from leafcutter.

from leafcutter.

Thank you.
posting below:

Running differential splicing analysis...
Differential splicing summary:
statuses Freq
1 Success 523
2 <=1 sample with coverage>min_coverage 7
3 Not enough valid samples 71
4 <2 introns used in >=min_samples_per_intron samples 1
Saving results...
No exon_file provided.
Warning message:
In bind_rows_(x, .id) : Unequal factor levels: coercing to character
All done, exiting

from leafcutter.

from leafcutter.

Yes, this is correct.

from leafcutter.

I was getting the same error. I believe you need to use tryCatch instead of try

from leafcutter.

I'll take a look at this now.

from leafcutter.

Ok, should be fixed now. Thanks for pointing the issue out and let me know if you have any more problems!

from leafcutter.

Thanks so much!

from leafcutter.

Hi, could it be that this line is causing the path to be such:
args = strsplit( c("--num_threads 4 -e ../leafcutter/data/gencode19_exons.txt.gz ../example_data/testYRIvsEU_perind_numers.counts.gz ../example_data/test_diff_intron.txt"), " ")[[1]],
positional_arguments = 2)
I am getting errors. I don't have administrator privileges, so I am waiting for the software to be updated on our cluster. But this looks like it could be the error.
Even running -h for help I get:
/home/aeskin/leafcutter/scripts/leafcutter_ds.R -h
Loading required package: Rcpp
Warning messages:
1: replacing previous import by 'stats::filter' when loading 'leafcutter'
2: replacing previous import by 'stats::lag' when loading 'leafcutter'
3: 'Rcpp::loadRcppModules' is deprecated.
Use 'loadModule' instead.
See help("Deprecated")
Loading counts from ../example_data/testYRIvsEU_perind_numers.counts.gz
Error: File ../example_data/testYRIvsEU_perind_numers.counts.gz does not exist
Execution halted

Thanks!

from leafcutter.

Ugh yes good spot. Fixed now!
By the way, you should be able to install without admin privileges, you can always install R packages to a local directory (i.e. somehow under your home directory on your cluster).

from leafcutter.

Thank you and thanks for the tip!
Sorry to be a pain! =)
But I am getting this error that I didn't get previously:
/home/aeskin/leafcutter/scripts/leafcutter_ds.R --num_threads 4 /home/aeskin/leafcutter/example_data/testYRIvsEU_perind_numers.counts.gz /home/aeskin/leafcutter/example_data/test_diff_intron.txt

Running differential splicing analysis...
Error in differential_splicing(counts, numeric_x, confounders = confounders, :
unused argument (confounders = confounders)
Execution halted

Thanks again!

from leafcutter.

I think this is because you have the new leafcutter_ds.R script but the package hasn't been reinstalled yet. Can you try installing the package locally - I think you just need to do e.g.
install_github("davidaknowles/leafcutter/leafcutter", lib="~/myRlibs/")
or wherever in your home dir you want to put personal packages.

from leafcutter.

Thanks so much, it works, and with the annotation!

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