nchernia
commented
3 years ago Hello,
We don't have a PBS system and so cannot test the tool. We didn't write the "nonsites" script, but I think you should just get rid of all the backslashes. If that works, please submit the updated file as a pull request.
Thanks! Neva
On Wed, Mar 3, 2021 at 2:16 PM Dustin Sokolowski notifications@github.com wrote:
Hello!
Thank you for the fantastic tool. I am aligning some Hi-C data to a de novo genome our lab is creating using the PBS version of juicer and I think that there is a syntax error in the "chimeric_nonsites.awk" script.
I think that this is an error because when I run the script I get the following error:
awk -f /hpf/tools/centos7/juicer/1.6/scripts/chimeric_nonsites.awk NMR_Fibroblast_HiC_test.txt > NMR_Fibroblast_HiC_test.frag.txt
[image: image] https://user-images.githubusercontent.com/56414662/109858715-2b307a00-7c2a-11eb-9ca2-f517a87cc547.png
Alternatively, when I go onto the CPU version of juicer and run the original awk script, it has been running for over an hour and has been producing a reasonable output
awk '{printf("%s %s %s %d %s %s %s %d", $1, $2, $3, 0, $4, $5, $6, 1); for (i=7; i<=NF; i++) {printf(" %s",$i);}printf("\n");}' NMR_Fibroblast_HiC_test.txt > NMR_Fibroblast_HiC_test_frag.txt
[image: image] https://user-images.githubusercontent.com/56414662/109858896-62069000-7c2a-11eb-8d05-6ca0cf12030f.png
Accordingly, I think that there is a bug in this new awk script.
I have attached the "NMR_Fibroblast_HiC_test.txt" file, which is the first 1000 lines of my *_norm.txt file to all you to try and re-produce the error. If you cannot re-produce it then perhaps the error is in how our directories are structured and I would love some help with that as well!
In terms of where I am running juicer: https://ccm.sickkids.ca/high-performance-computing/
Thank you so much, Dustin
NMR_Fibroblast_HiC_test.txt https://github.com/aidenlab/juicer/files/6078573/NMR_Fibroblast_HiC_test.txt
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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org
DustinSokolowski
Hello!
Thank you for the fantastic tool. I am aligning some Hi-C data to a de novo genome our lab is creating using the PBS version of juicer and I think that there is a syntax error in the "chimeric_nonsites.awk" script.
I think that this is an error because when I run the script I get the following error:
awk -f /hpf/tools/centos7/juicer/1.6/scripts/chimeric_nonsites.awk NMR_Fibroblast_HiC_test.txt > NMR_Fibroblast_HiC_test.frag.txtAlternatively, when I go onto the CPU version of juicer and run the original awk script, it has been running for over an hour and has been producing a reasonable output
awk '{printf("%s %s %s %d %s %s %s %d", $1, $2, $3, 0, $4, $5, $6, 1); for (i=7; i<=NF; i++) {printf(" %s",$i);}printf("\n");}' NMR_Fibroblast_HiC_test.txt > NMR_Fibroblast_HiC_test_frag.txtAccordingly, I think that there is a bug in this new awk script.
I have attached the "NMR_Fibroblast_HiC_test.txt" file, which is the first 1000 lines of my *_norm.txt file to all you to try and re-produce the error. If you cannot re-produce it then perhaps the error is in how our directories are structured and I would love some help with that as well!
In terms of where I am running juicer: https://ccm.sickkids.ca/high-performance-computing/
Thank you so much, Dustin
NMR_Fibroblast_HiC_test.txt