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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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outrigger --index error: "AttributeError: 'Series' object has no attribute 'iteritems'" #104

Open jordimaggi opened 1 year ago

jordimaggi commented 1 year ago

Hi,

I am running outrigger for the first time. I am running it on an RNA-seq dataset aligned with STAR, which resulted in a .bam file of 3.6 GB and a corresponding SJ.out.tab file of 14.6 MB.

I used the following command:

outrigger index --sj-out-tab *SJ.out.tab --gtf hg19.ensGene.gtf

I obviously forgot to check if there was an option to use multiple cores to run the command. Therefore, it successfully ran for 5 days, up to the Making ".bed" files for exons in each event ... step, which failed due to the following error:

AttributeError: 'Series' object has no attribute 'iteritems'

Any idea on how to fix this? Also, can I re-start the command without repreating the steps that it was able to complete? If so, how?

Thanks for your help.

The conda environment that I am using to run the command has the following packages installed:

outrigger_packs2

khksw0403 commented 1 year ago

Hi, All. i got same issue. i tested latest and 1.0.0 version.