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SIGSEGV during Augustus PB step on test data #118
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I have not encountered the wiggletools test data issues before, but I doubt it is a big deal. Wiggletools are only used for generating tracks for the final assembly hub, and so won't effect the actual annotation results. Thank you for providing the input files to augustus! I just tried it myself using your input files and it seems to work fine.
I did this with a augustus binary compiled from commit Regardless, I think the next step is to open an issue on the augsutus repository with these inputs and with information about your build. |
Thanks for the super quick reply! I might try recompiling and giving it another go just in case something went awry. I'll let you know how it goes. |
No worries, let me know how it goes. I did my test on a Ubuntu machine. |
Wooo! It does seem that it was something to do with difficulties in installing Augustus locally, because the cluster folks reinstalled an updated version and it worked. I'm going to attach my stream-of-consciousness of getting c-a-t installed below just in case it helps anyone else on an HPC system, and I'll post the Augustus easy build log on my issue over there. Thanks for all your help Ian!
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@laninsky thank you for sharing this! It helped a lot :-) |
Glad it helped @dandaman! |
Hi folks,
Apologies if I've missed something dumb during installation here, but I'm a bit stuck. I'm running cat on a slurm system, but using a single machine just to try and minimise complications:
It seems to get through the Augustus CGP step fine, but then fails with a SIGSEGV on the Augustus PB step
Running the command outside of cat also gives a Segmentation Fault. From previous issues I thought filename length could be an issue, so I copied out the offending files and renamed them (also attached here with the modified names), but still ran into the same issue running it outside of cat:
extrinsicCfgFile.tmp.txt
hintsfile.tmp.txt
input.tmp.txt
I followed the instructions for compiling Augustus CGP from https://github.com/Gaius-Augustus/Augustus (from yesterday or the day before's git version - I've tried getting cat installed multiple times over the last few weeks, so this was a fresh attempt), have used the pre-compiled kent binaries, and I'm using modules for Samtools (1.8), bamtools (2.4.1), bedtools (2.26.0). The only thing that seemed "off" during installation was that wiggletools failed some of its tests (however, a google suggested this could be because of reference mismatches between the bam and cram files):
Any help would be really appreciated.
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