R session aborts with featureCounts

[J Summe]

Hello,

I'm using Rsubread version 2.0.1 and trying to run featureCounts with a BAM file produced by the align function in Rsubread. I've attached the .bam file and the .gtf file that I'm using to count against. Every time I've tried to run this command in Rstudio, the R session aborts. I'm using just one of the my 31 bam files to troubleshoot and have tried a few others but it still results in an error.

Any help would be much appreciated!

Here are the first few lines of the .gtf file:

10000048        transdecoder    gene    1       514     .       -       .       gene_id "GENE.10000048~~10000048.p1"; gene_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24";
10000048        transdecoder    mRNA    1       514     .       -       .       transcript_id "10000048.p1"; gene_id "GENE.10000048~~10000048.p1"; transcript_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24";
10000048        transdecoder    exon    1       514     .       -       .       gene_id "10000048.p1.exon1"; transcript_id "10000048.p1.exon1"; exon_number "1"; gene_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24"; transcript_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24";
10000048        transdecoder    CDS     14      514     .       -       0       gene_id "cds.10000048.p1"; transcript_id "cds.10000048.p1"; gene_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24"; transcript_name "ORF%20type%3A5prime_partial%20len%3A167%20%28-%29%2Cscore%3D8.24";
10000048        transdecoder    three_prime_UTR 1       13      .       -       .       three_prime_UTR_id "10000048.p1.utr3p1"; transcript_id "10000048.p1";
                                                                ";
10000534        transdecoder    gene    1       299     .       +       .       gene_id "GENE.10000534~~10000534.p2"; gene_name "ORF%20type%3Ainternal%20len%3A100%20%28%2B%29%2Cscore%3D21.72";
10000534        transdecoder    mRNA    1       299     .       +       .       transcript_id "10000534.p2"; gene_id "GENE.10000534~~10000534.p2"; transcript_name "ORF%20type%3Ainternal%20len%3A100%20%28%2B%29%2Cscore%3D21.72";
10000534        transdecoder    exon    1       299     .       +       .       gene_id "10000534.p2.exon1"; transcript_id "10000534.p2.exon1"; exon_number "1"; gene_name "ORF%20type%3Ainternal%20len%3A100%20%28%2B%29%2Cscore%3D21.72"; transcript_name "ORF%20type%3Ainternal%20len%3A100%20%28%2B%29%2Cscore%3D21.72";
10000534        transdecoder    CDS     3       299     .       +       0       gene_id "cds.10000534.p2"; transcript_id "cds.10000534.p2"; gene_name "ORF%20type%3Aint

[J Summe]

Sorry here are the commands I ran:

bams<-list.files(path=".",pattern="bamfile.bam")

featureCounts(files=bams, annot.ext=gtf,isGTFAnnotationFile=TRUE, isPairedEnd=TRUE, nthreads=2, autosort=TRUE)

[Yang LIAO]

Thanks for the bug report, but I cannot find the attachments to your post. If the files are too large, you may consider sharing them using OneDrive/Dropbox/etc. I can also create a cloud sharing space so you can upload your BAM file into it.

The first few lines in your GTF file seem OK and your commands are correct. 

[J Summe]

Hi thank you ! Here is a link to the bam file I was using:

https://liveutk-my.sharepoint.com/:u:/g/personal/jsumme24_vols_utk_edu/EVGn8S4_zitAsXvuVx4UdQgBp9oNEjfBIbgwQ9sNqm8uvw?e=JSIFzw

Let me know if there are any issues. Thank you again for your help!

[Yang LIAO]

Thank you, Summe. I have downloaded it and you may delete the shared file.

However, I didn't have any errors when I used Rsubread-2.0.1 to count your BAM file. The program finished smoothly. Because you didn't share your GTF file, I used a random GTF file in my test.

Can you also share your GTF annotation?

[Yang LIAO]

Also, can you provide the sessionInfo() output in Rstudio?

I hope to know the architecture of the system and the R version, etc.

[J Summe]

Yes, here's the sessionInfo()

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rsubread_2.0.1

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0    knitr_1.28     xfun_0.14

[Yang LIAO]

Thanks, Summe. I have had your GTF file. This GTF file has many lines that don't follow the GTF format. For example, the 6th line is nothing but TABs, a quotation mark, and a semicolon. 

After removing these lines, featureCounts was able to produce read counts on it.