Does one need short read? Also not giving -sr still invokes short read?

[jychoilab]

Hello

It wasn't clear to me that whether short reads were necessary for Lorean?
I have long read sequencing RNA data but no short reads. I ran the example dataset without the short read and it seems to work albeit it missing some genes. I can live with that for now.
But whats strange is I executed Lorean on my real data without the -sr flag and in the stdout I get the message

###BRAKER1 (USING SHORT READS) AND EXONERATE STARTED AT:

Note when I used the example dataset and command without the -sr flag I didn't see the message.
Right now its at the step

###RUNNING DIAMOND ###

so I'm going to wait and see what happens but I seem to have gotten a core dump at somepoint as well since I see a file 'core.102659'.

Any ideas what might be happening?

Thanks in advance for the help!

[lfaino]

Hi @cjy8709,
can you send me command of lorean that you run?

Cheers
Luigi

[jychoilab]

Yup I ran it as:

singularity exec -B /home/jyc387/PROGRAMS_AND_SCRIPTS/PROGRAMS/LoReAn/config/:/opt/LoReAn/third_party/software/augustus/config/ -B /home/jyc387/PROGRAMS_AND_SCRIPTS/PROGRAMS/LoReAn/Libraries/:/usr/local/RepeatMasker/Libraries/ lorean_latest.sif lorean \
-a -t 20 --keep_tmp -d \
-lr 20200313-5FFAL74730-5FDD.3.2.10.hac.full_length_output.fastq \
-pr Mpol2.prot.fa \
-sp MetPol \
Ref_genome.flye.uncorrected_raw.filter_MinLength10k_MinMeanQ85_MinWindowQ70.fa

[lfaino]

The idea is that with long reads, the tool works anyway.

can you try to pull the image with name:

lfaino/lorean:repetmodeller

and run it to see if you ge the same error?

thanks
Luigi