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TRON-Bioinformatics / EasyFuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
GNU General Public License v3.0
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Tool runtime #22

Open BGI2016 opened 1 year ago

BGI2016 commented 1 year ago

Hello @ibn-salem @priesgo @ozlemmuslu @martinloewer @mostafiz2010 My data is 260 million distinct sequencing reads（2×150 nt）.When I predicted GFs with the Easyfuse 1.3.6 from my data, the software ran for eight days. why run time is so long?Hope to get your reply.

Kind Regards, Lily

Tesson98 commented 1 year ago

Hi @ibn-salem @priesgo @ozlemmuslu @martinloewer @mostafiz2010

I have also met this problem with paried rna-seq fastq.gz files of 29 samples(2 ~3G 29samples). Within them 24/29 succeed in the output but the remaining 5 samples were stuck in the soapfuse prediction step (4 samples, succeed in upstream prediction steps) or in the fetchdata step ( 1 sample, succeed in upstream steps). I have to ended related slurm jobs while running for 7 days. Could you help me with this problem？

Really glad to get your replies. If you want more detailed information please just contact me. Thank you so much!

Best regards, Tesson

whiffen-cann commented 1 year ago

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@Tesson98 @priesgo I also encounter the same problem. When I use Docker to run EasyFuse, I always report an error in the fetchdata.py step.

pintoa1-mskcc commented 1 year ago

I also encounter extremely long run times, and then soapfuse will die randomly....