Official Repository of the Oyster River Protocol for Transcriptome Assembly
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assemblies/
folder at the end of the run.
Hi @54mu,
This is a known issue, as it sometimes gets hung on this step. This step does take a while, but I'd say this one is definitely hung. I'd kill this job and start again.
A corollary issue is that 200M reads is a lot, and it will pretty dramatically increase the memory/time needed, particularly at this step.
How much memory are you giving the job? And what version of the ORP/SPAdes are you running? Memory issues used to be an issue with SPAdes, but that hasn't been the case for a year or two.
hi, I would like to point out some issues and relative fixes I found. first -this is mainly related to trinity and transabyss- raw reads from SRA are often refused by Trinity for their name and simply discarding the names doesn't work well for trinity and transabyss (i guess it's about how they perform the scaffolding process). To fix this a simple bash script like this should work:
#!/bin/bash
#read file names need to be formatted as filename.1.fastq.gz/filename.2.fastq.gz
read=$2
filename=$(basename -- "$1")
extension="${filename##*.}"
filename="${filename%.*.*.*}"
zcat $1 | awk '{{print (NR%4 == 1) ? "@'$filename'_" ++i "/'$read'": $0}}' > $filename.$2.fastq
Another issue is relative to the transrate step, this happened when i was using a very large number of reads as an input (>500.000.000). I don't know much about ruby, but for some reason it was failing to remove some temporary folders and they were not empty. This was fixed by changing line 145 of /mnt/DATA/Software/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/snap.rb:
#from
Dir.delete(@index_name) if Dir.exist?(@index_name)
#to
require 'fileutils'
FileUtils.rm_r @index_name if Dir.exist?(@index_name)
I hope this will be helpful if someone stumbles on the same issues
Hi all,
First of all, thanks so much for the ORP. Really neat idea, and very nice coding. I was wondering if there is any way I can add multiple R1 and R2 files to the READ1 and READ2 flags. I tried doing so by separating the file paths with commas, but I get the following error message:
* Welcome to the Oyster River *
* This is version 2.2.6 *
ERROR: YOUR READ1 FILE DOES NOT EXIST AT THE LOCATION YOU SPECIFIED
/bin/bash: shell: command not found
/home/orp/Oyster_River_Protocol/oyster.mk:156: recipe for target 'readcheck' failed
make: * [readcheck] Error 127
Here's how I called ORP:
orp_path=/home/orp/Oyster_River_Protocol
$orp_path/oyster.mk STRAND=RF \
TPM_FILT=1 \
MEM=40 \
CPU=10 \
READ1=$folder_path/39_b_S8.1.fq,$folder_path/39_o_S6.1.fq \
READ2=$folder_path/39_b_S8.2.fq,$folder_path/39_o_S6.2.fq \
RUNOUT=full_out
Hi Matt, question re the use of diamond in ORP. I've found that diamond blast searches block certain neuropeptides that I know are expressed (via antibody labeling) because of a repeat-sequence masking option. When I turn that off, I can then recover these sequences. I noticed this blasting ORP assemblies, but have now realized/remembered that diamond is part of ORP. I couldn't find the specific diamond command that I think is used after Orthofinder(I know where to change the diamond command for Orthofinder itself).
Basically, I'm thinking of re-running ORP after changing diamond just to check whether it makes a difference for assembly...
Hi @macmanes I'm trying to run orthofuser.mk on a set of transcriptomes (same species) that have been generated using the Oyster River Protocol (ORP). I'm running a docker container that has the most up-to-date version of ORP pulled from the master channel on an Ubuntu 18.04 server. The ORP generated transcriptomes were generated on the same container. Following renaming I tried to run the orthofuser.mk snakemake file, and the program runs for some time before failing. The error I receive isn't so revealing to me:
/home/orp/Oyster_River_Protocol/orthofuser.mk:68: recipe for target '/home/orp/assemblies/merge.orthomerged.fasta' failed
make: *** [/home/orp/assemblies/merge.orthomerged.fasta] Error 1
Please let me know if any additional info might be useful for determining why the script is failing.
Hello, I am trying to install ORP on an AWS server. I encountered the following issues:
AWS Ubuntu Server 20.04
1) Installed ORP using docker option 1 (sudo).
2) chmod -R 777 transferData
3) Tweaked the following statement: docker run -it \
--mount type=bind,source=/home/ubuntu/,target=/home/orp/docker \
macmaneslab/orp:2.2.6 bash
New:
docker run -it \
--mount type=bind,source=/home/ubuntu/transferData/,target=/home/orp/docker \
macmaneslab/orp:2.2.6 bash
4) Started ORP
$HOME/Oyster_River_Protocol/oyster.mk \
STRAND=RF \
TPM_FILT=1 \
MEM=128 \
CPU=32 \
READ1=All_R1_Reads.fastq.gz \
READ2=fixed_R3_reads.fastq.gz \
RUNOUT=test
4) ORP crashed. Error dealing with "pipeliner"
I am new to gitter and orp. Is there a way to post the screen shots that I took?
Since this was a dead end for me then I tried a different option. However that didnt work either. Here is what I did:
Installation WITHOUT docker
new instance. this time with an AWS ubuntu server 16.0 , specifications as before (290 hdd, 32 vcpus 128 gb ram)
Installation was successful. Test run was terminated at the very end(!) causing the following error:
/home/ubuntu/Oyster_River_Protocol/oyster.mk:365: recipe for target '/home/ubuntu/Oyster_River_Protocol/sampledata/assemblies/test.ORP.fasta' failed
make: * [/home/ubuntu/Oyster_River_Protocol/sampledata/assemblies/test.ORP.fasta] Error 1
Changed permissions with chmod -R 777 sampledata
This time ORP crashed right away!
Exactly the same error message as before
/home/ubuntu/Oyster_River_Protocol/oyster.mk:365: recipe for target '/home/ubuntu/Oyster_River_Protocol/sampledata/assemblies/test.ORP.fasta' failed
make: * [/home/ubuntu/Oyster_River_Protocol/sampledata/assemblies/test.ORP.fasta] Error 1
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!