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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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cnv-calculate Runtime Error #7

Closed wzhang42 closed 3 years ago

wzhang42 commented 3 years ago

Hi, XiaoTao, I am now playing with the NeoLoopFinder. I use your provided demo .cool file to cnv-calculate, it's ok. But I use my own .cool file, it always report the following Runtime error.

Traceback (most recent call last): File "/home/wzhang/.conda/envs/neoloop/bin/calculate-cnv", line 128, in run table = runcnv.signal_from_bigwig(table, gc_fil, name='GC') File "/home/wzhang/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/cnv/runcnv.py", line 50, in signal_from_bigwig v = bw.stats(row['chrom'], row['start'], row['end'], type='mean')[0] RuntimeError: Invalid interval bounds!

The Command lines for the two case are the following: calculate-cnv -g hg38 -H K562-MboI-allReps-hg38.10K.cool --output ./calculate-cnv.txt -e MboI --cachefolder ./neoloopfinder (It's ok) calculate-cnv -g hg38 -H hic_SH-SY5Y.inter_10000.cool --output ./calculate-cnv.txt -e MboI --cachefolder ./neoloopfinder (Runtime Error) Could you please provide me some clues to fix this RuntimeError? Additionally, I use hicConvertFormat to convert .hic to the cool format. The command is the following: hicConvertFormat -m ./hic_SH-SY5Y.inter.hic --inputFormat hic -o hic_SH-SY5Y.inter.cool --outputFormat cool --resolution 10000

Look forward to hearing from you Thank you in advance.

XiaoTaoWang commented 3 years ago

Hi, can you check issue #1, and let me know if it works after adding "chr" to your cool files.

wzhang42 commented 3 years ago

Xiaotao, Thank you so much. It seems work.