Price error Input not sorted on sorted BAM file

erhard-lab / gedi

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Price error Input not sorted on sorted BAM file #15

Closed pkohvaei closed 1 month ago

pkohvaei commented 1 month ago

Dear Florian,

Here I include the command and the relevant part of the output:

gedi -e Price -reads test_2.sortedS.bam -genomic homo_grch38109 -prefix price -progress -plot

Error:
java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceClusterReads@576239a2
Could not run gedi.riboseq.javapipeline.PriceClusterReads@576239a2
Input not sorted: 1+:629089-629119      [1] x2 0|30|0   3pGACATCCGTGGTAGTTGr > 1+:629088-629119 [3] x2 2|29|0   3pGACATCCGTGGTAGTTGr

Using Gedi version 1.0.6a .

Thank you

florianerhard commented 1 month ago

The bam file is not correctly sorted. Please use bamlist2cit to convert to cit, this should do the trick! F

pkohvaei commented 1 month ago

The next step we used bamlist2cit and re-ran. Now the tool goes till ORF inference and there throws this error:

2024-07-19 10:50:40.794 INFO Starting PriceOrfInference ...
2024-07-19 10:50:41.107 INFO Infer ORFs
PRICE
PRICE is an analysis method for Ribo-seq data.

Error:
java.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceOrfInference@1e440333
Could not run gedi.riboseq.javapipeline.PriceOrfInference@1e440333
Exception in parallel iterator thread!
Index 0 out of bounds for length 0

Here I include the files the pipeline has created up to the exit point (hope it helps):

Thanks a lot.

pkohvaei commented 1 month ago

I go ahead and move the second step into a new issue.