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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Segmentation fault (core dumped) #27

Closed sateeshperi closed 4 years ago

sateeshperi commented 4 years ago

Hi, I am facing the following error reported in other issues as well....attaching my error log as well.....any help in debugging this would be great.

MAIN: STATUS: iteration, slaves_processed, new_matches, slave_to_match_relation, targets_needed, targets_collected MAIN: STATUS: 4, 1, 1128, 1128, 0, 0, 2020/03/02 15:43:38 MAIN: starting iteration 5 WORKQUEUE: matches collected. FW: 0 REV: 0 MAIN: 0 new matches collected MAIN: nothing changed, skipping cycle and waiting 3 seconds ERROR: NEW Match received from slave 1 saved to position 1 looks wrong! : 64/72 bytes received : query_id=80 : target_id=5 : query_size=19988679 : qstart=4763964 : tstart=4695395 : len=290 : reverse=0 : prob=1 : ident=0.603774 MAIN: starting iteration 5 WORKQUEUE: matches collected. FW: 12 REV: 1855 MAIN: 1867 new matches collected MAIN: Running the chaining step... Matches before collapse: 237063 Matches after collapse: 236967 MAIN: running coverage tracker MAIN: coverage tracker: +60535420 -8552 MAIN: DynProg... Chaining (inline)... Filling out repeat lists... Segmentation fault (core dumped) satsuma2_error_log.txt

jonwright99 commented 4 years ago

Hi Sateesh, This sounds like the same issue others have been having, probably due to your network configuration and satsuma slaves not being able to connect to the master process. To try to get around this we created a set of prebuilt binaries for Satsuma2 that you can download, copy to a directory on your HPC and run without compiling. The previous user who had this problem never got back to me about it so we were never able to test it. You can download the gzipped binaries here - https://github.com/bioinfologics/satsuma2/releases. Let me know if these work.

sateeshperi commented 4 years ago

@jonwright99 It works with the new binaries. Thanks for the response

jonwright99 commented 4 years ago

Great, glad these worked.