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macmanes-lab / Oyster_River_Protocol

Official Repository of the Oyster River Protocol for Transcriptome Assembly
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Issue with SPADES2/Kmer length #44

Open chiroptera19 opened 3 years ago

chiroptera19 commented 3 years ago

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 $(firstword $(MAKEFILE_LIST))) 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: macmanes-lab/Oyster_River_Protocol#17

Was this ever resolved/addressed? How can I get ORP to run for reads that are 75bp or less? Hoping to hear back!

macmanes commented 3 years ago

sorry, yes this has been updated in the most recent release.