search

nerettilab / RepEnrich2

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
36 stars 9 forks source link

RepEnrich2_subset.py rna-seq PE error #16

Closed Runuply closed 5 years ago

Runuply commented 5 years ago

Hi Nick

RepEnrich2 works well when I am using the SE rna-seq data, however, if I use the PE, the RepEnrich2_subset.py script is crashed. Could you please let me know the solution?

Thanks,

Screen Shot 2019-07-03 at 2 48 08 PM Screen Shot 2019-07-03 at 3 08 59 PM
nskvir commented 5 years ago

Is there any other output, or just the symbols above? If the script isn't throwing a specific error message it's hard to discern what the problem is without being able to reproduce the issue on my end.

Runuply commented 5 years ago

There are outputs of filtered.bam and unique.bam, except for the multimap.fastq. There is no specific error but only the running symbols. However, the single end data work well without any issue from beginning to the end.

Screen Shot 2019-07-08 at 3 07 54 PM

nskvir commented 5 years ago

It looks like it was in the process of sorting the bam file when the error occurred (although there should be a print statement that happens before that, which I do not see in your first screenshot). Can you tell me what version of samtools you have installed?

Runuply commented 5 years ago

samtools 1.2 Using htslib 1.2.1 Copyright (C) 2015 Genome Research Ltd.

nskvir commented 5 years ago

I would start by trying a newer version of Samtools (v1.3.1 was what I used when I wrote the tutorial) in case there is some functionality that differs in the older versions.

Also be sure the other versions of dependencies are all up to date as well -- versions of all the software I use are as follows: Python version 2.7.12+, Bedtools version 2.25.0, Bowtie2 version 2.2.9, Samtools version 1.3.1, and BioPython version 1.66-py2.7.

Let me know if this helps!

Runuply commented 5 years ago

Thanks, It is working well after updating the samtools.