Issue with SPADES2/Kmer length #44
Description
Hello! I absolutely love the ORP and have run it successfully with a lot of my reads. However, I'm running into quite the head scratcher for reads that are 75 bp long or less. The program documentation says you can specify your SPADES2_KMER=INT length, which I have done in the following lines:
MAKEDIR :=
DIR := ${CURDIR}
CPU=16
BUSCO_THREADS=${CPU}
MEM=110
TRINITY_KMER=25
SPADES1_KMER=55
SPADES2_KMER=35
TRANSABYSS_KMER=32
RCORR := ${shell which rcorrector}
My reads are exactly 75 bp long, but changing the SPADES2_KMER flag does not resolve the issue. I still receive the following error:
IT LOOKS LIKE YOUR READS ARE NOT AT LEAST 75 BP LONG,
PLEASE EDIT YOUR COMMAND USING THE SPADES2_KMER=INT FLAGS,
SETTING THE ASSEMBLY KMER LENGTH LESS THAN YOUR READ LENGTH
/bin/bash: line 8: shell: command not found
I found a discussion about this on the github from 2019: #17
Was this ever resolved/addressed? How can I get ORP to run for reads that are 75bp or less? Hoping to hear back!