search

BosingerLab / BALDR

MIT License
7 stars 8 forks source link

STAR shared memory does not work in the cluster environment #11

Closed tAndreani closed 4 years ago

tAndreani commented 4 years ago

Hello,
i am trying to run BALDR in the HPC environment but I have an issue related to the shared memory. (https://github.com/alexdobin/STAR/issues/841). I am wondering if there is a way to disabilitate that in BALDR. Given that you provide only one command (https://github.com/BosingerLab/BALDR), I do not see where there is the option to disabilitate the "shared memory" of STAR (that is also suggested in some cases).

this is my command: 

./BALDR --paired no92_RL0659_D2_1.fastq.gz,no92_RL0659_D2_2.fastq.gz --trinity /path/Trinity --adapter /path/NexteraPE-PE.fa --trimmomatic  /path/trimmomatic-0.32.jar --igblastn /path/igblastn --STAR /site/ne/app/x86_64/star/v2.5.2b/STAR 
--STAR_index /path/BALDR-master/STAR_GRCh38/STAR_GRCh38_index  --BALDR /path/BALDR --memory 40 --threads 2

and this is the error: 

Shared memory error: 4, errno: Invalid argument(22)
EXITING because of FATAL ERROR: problems with shared memory: error from shmget() or shm_open().
SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory

Thank you in advance for any reply. Best

amit-upadhyay commented 4 years ago

Hello,

I have changed the default to NoSharedMemory for STAR command. The LoadAndKeep option will be used when the --sharedMemory flag is specified. You can pull the changes and try again.

Thanks for the feedback. Best.

tAndreani commented 4 years ago

Thank you, now it works. I have another issue: 

Error, do not understand options: --no_normalize_reads --output IG-mapped_Unmapped/Trinity/no92_RL0659_D2_1.IG-mapped_Unmapped_trinity

I am using this version of Trinity Trinity v2.0.6. Do you know if a older version of the one reccomended is preventing Trinity to work? You mention that new versions in respect of the one reccomended do not work. Before open new thickets I want to be sure about this.

Actually I have solved this just using the version reccomended. I would like to mention also the the tool fastool is required to run BALDR. I did this with anaconda: conda install -c bioconda fastool

Best

amit-upadhyay commented 4 years ago

I will look into the fastool dependency. My guess is that a newer version of one of the tools in the pipeline may have the fastool requirment. Thank you for pointing this out.