search

nerettilab / RepEnrich2

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

Got stuck with RepEnrich2 #26

Closed matwgmkw closed 1 year ago

matwgmkw commented 1 year ago

Hi. I got stuck while using RepEnrich2. Here is the error message I got. How can I fix it?

Software versions I used: py-biopython/1.70_py27 bedtools/2.27.1 bowtie2/2.3.4.1 samtools 1.16.1 Python 2.7.13

Thanks. Matthew

Preparing for analysis using RepEnrich2... Conducting region sorting on unique mapping reads.... ***** WARNING: File ./RepEnrich2_setup_hg38/repnames.bed has inconsistent naming convention for record: chr1 10469 11447 TAR1

***** WARNING: File ./RepEnrich2_setup_hg38/repnames.bed has inconsistent naming convention for record: chr1 10469 11447 TAR1

Identified 0 unique reads that mapped to repeats. Processing repeat psuedogenomes... sorting and combining the output for both read pairs... completed ... Writing and processing intermediate files... Traceback (most recent call last): File "RepEnrich2.py", line 269, in for data in importtext(sorted + os.path.sep + rep + '.txt', '\t'): File "RepEnrich2.py", line 64, in import_text skipinitialspace=True): _csv.Error: line contains NULL byte

matwgmkw commented 1 year ago

I got the "regionsorter.txt" file with some data in it, but that is the only file I got after running RepEnrich2.

matwgmkw commented 1 year ago

Another question is if I downloaded the setup for the human genome from the dropbox link (https://www.dropbox.com/sh/ovf1t2gn5lvmyla/AADEPGgGMg-vjj8Gk-s76i6Ja?dl=0), do I still have to do the setup in step 2?

nskvir commented 1 year ago

Hi there,

The setup folder is meant to save some time and should let you skip the setup step, but it seems like something might have been changed inside repnames.bed - maybe an extra tab or some white space was added to the line in question? If it still doesn't work after checking this, I would advise just starting from the first step and attaining fresh annotation files from UCSC table browser and running the setup yourself as opposed to using the dropbox folder. That should give you a fresh setup folder that should work with whatever annotation you provide it.

Best, Nick