Issue with executable orgasmi - Tutorial fails
The tutorial as described at https://pythonhosted.org/ORG.asm/mitochondrion.html does not work under the current version of ORG.asm.
$ oa index --estimate-length=0.9 butterfly papi_R1.fastq.gz papi_R2.fastq.gz --no-pipe
2018-10-24 19:22:57,219 [INFO ] Indexing in no pipe mode
2018-10-24 19:22:57,390 [INFO ] orgasmi -o butterfly.odx/index /tmp/tmpqrlg1lij/forward-23i3_782 /tmp/tmpqrlg1lij/reverse-q2_o7wyv
2018-10-24 19:22:57,390 [INFO ] Writting transformed sequence files...
2018-10-24 19:22:57,390 [INFO ] Forward tmp file : /tmp/tmpqrlg1lij/forward-23i3_782
2018-10-24 19:22:57,390 [INFO ] Reverse tmp file : /tmp/tmpqrlg1lij/reverse-q2_o7wyv
2018-10-24 19:22:57,390 [INFO ] Selecting the best length to keep 90.0% of the reads.
2018-10-24 19:22:57,390 [INFO ] Minimum length set to 0bp
2018-10-24 19:22:57,390 [INFO ] Soft clipping bad quality regions (below 10).
2018-10-24 19:22:57,390 [INFO ] Select the longest region containing only [A,C,G,T]
2018-10-24 19:22:57,390 [INFO ] Two files pair-end data
Read length estimate [ 32768] speed : 110120.5 reads/s
2018-10-24 19:22:57,833 [INFO ] Indexing length estimated to : 100bp
2018-10-24 19:22:58,623 [INFO ] Done.
2018-10-24 19:22:58,623 [INFO ] Starting indexing...
2018-10-24 19:22:58,623 [INFO ] orgasmi -o butterfly.odx/index /tmp/tmpqrlg1lij/forward-23i3_782 /tmp/tmpqrlg1lij/reverse-q2_o7wyv
Reading sequence reads...
2018-10-24 19:22:58,947 [INFO ] 47371 reads pairs processed
2018-10-24 19:22:58,948 [INFO ] 0 reads pairs soft trimmed on a quality of 10
2018-10-24 19:22:58,948 [INFO ] 0 reads pairs clipped for not [A,C,G,T] bases
[src/load.c:40] ERROR : Cannot open file butterfly.odx/index.ogxSpecifically, it seem that the code underlying the executable "orgasmi" is broken, as calling that executable results in a segmentation fault:
orgasmi -o butterfly.odx/index /tmp/tmpqrlg1lij/forward-23i3_782 /tmp/tmpqrlg1lij/reverse-q2_o7wyv
Reading sequence reads...
Segmentation fault (core dumped)Info of system on which the above was tested:
$ uname -a
Linux user 4.18.12-arch1-1-ARCH #1 SMP PREEMPT Thu Oct 4 01:01:27 UTC 2018 x86_64 GNU/Linux