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I submitted this command to run the second part of tracula
trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt
And, before it would process, but then I was looking into SLURMS and somehow misconfigured it. Now I get:
I tried to reconfig the file and got it running again, but still get the error:
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(base) danielsalinas@danielsalinas-linux:~$ trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt
INFO: SUBJECTS_DIR is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer
INFO: Diffusion root is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri/nodif_brain_mask.nii.gz
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1 /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri
subjectdir is /home/danielsalinas/MRI-Data/Francis_HION/NCANDA-freesurfer/practice/freesurfer/tracula/output/NCANDA_S00033/dmri
Making bedpostx directory structure
Queuing preprocessing stages
srun: error: Invalid --mail-type specification
Queuing parallel processing stage
----- Bedpostx Monitor -----
srun: error: Unable to allocate resources: Job dependency problem
Queuing post processing stage
srun: error: Unable to allocate resources: Job dependency problem
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I remade the config file:
# Basic settings
ControlMachine=danielsalinas-linux
ClusterName=BakerLabCluster
AuthType=auth/munge
SlurmdPort=6818
SlurmctldPort=6817
SlurmUser=slurm
SlurmdUser=root
StateSaveLocation=/var/spool/slurmctld
SlurmdSpoolDir=/var/spool/slurmd
# Add or modify in your slurm.conf
JobCompType=jobcomp/filetxt
JobCompLoc=/var/log/slurm/jobcomp.log
# Node settings
NodeName=danielsalinas-linux CPUs=8 RealMemory=94000 Sockets=1 CoresPerSocket=4 ThreadsPerCore=2 State=IDLE
# Partition settings
PartitionName=normal Nodes=ALL Default=YES MaxTime=INFINITE State=UP