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hicup deduplicator error in read.table function #101

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WeiCSong opened this issue Feb 22, 2024 · 2 comments
Open

hicup deduplicator error in read.table function #101

WeiCSong opened this issue Feb 22, 2024 · 2 comments

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@WeiCSong
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Hi, thanks for the great tool! i'm running hicup on one pair of fastq input, and all pipelines go well until deduplicator step: all intermediate files until .filt.bam were generated successfully, but i got

Removing duplicates with HiCUP Deduplicator v0.6.1
De-duplicating fish-1m-4-11_21_S77_L002_R1_2_001.filt.bam
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.delim -> read.table
Execution halted

the output .hicup.bam, as well as the corresponding sumamry file, was empty. but it was surprising that the pipeline successfully ended afterward:

##error message on summary pie chart
De-duplication complete
Creating HTML and text file HiCUP summary reports #which is empty
HiCUP processing complete.

I'm not sure whether the pipeline has really finished, and would like to learn from you about possible solution. Alternatively, is it reasonable to directly use the .filt.bam file for downstream analysis, ignoring the de-duplication step? Thank you very much for your help.

@StevenWingett
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Hi,

I'm not sure what has happened here, but usually when HiCUP stops without explanation it is because not enough RAM was allocated for processing.

  1. Just checking, does HiCUP work on your system when processing the test dataset?

  2. Are you sure that HiCUP was working up until this de-duplication step? Are the intermediate BAM files large? Do the intermediate summary file contain acceptable results?

  3. If you try to process the data again with HiCUP, but specify more RAM (e.g. 50G), does it now work?

Best,
Steven

@WeiCSong
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Thanks for the information! HICUP do work on my system, and the .filt.bam and .pair.bam are large. truncator, mapper, and filter summary are also non-empty. I'll try to run with more RAM and see if it works.

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