"Error 1" possibly related to .newbies.fasta

[cooketho]

I'm getting the following error when running the command shown below. make: *** [/lab/pr/tc/sandbox/orp_test/assemblies/diamond/test.newbies.fasta] Error 1

I've attached the fastq files if you want to try and reproduce it. Maybe there's something wrong with the fastq? In any case, it would be helpful if ORP could output a more informative error message. fastq_files.zip

/lab/pr/tc/ORP/oyster.mk main \
STRAND=RF \
MEM=15 \
CPU=1 \
READ1=test.r1.fastq \
READ2=test.r2.fastq \
RUNOUT=test \
SPADES2_KMER=39 \
-d

[macmanes]

Hi,

This one was a little tricky, but is a result of there being only 1 gene KLF7 reconstructed by each assembler. Was this fastQ dataset intentionally reduced to serve as a test dataset?

[cooketho]

Yes, it is a reduced dataset for test purposes. Still, it should be able to handle that right?

[macmanes]

One can make a reduced dataset that is not representative of any real dataset, and then it's reasonably for the software to fail. I think this is what is happening here. No real transcriptome dataset would contain reads from only 1 transcript.

That being said, I will work on an enhancement that will provide a more informative error message that would cover this specific issue