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I submitted this command to run the second part of tracula trac-all -bedp -c $SUBJECTS_DIR/tracula/tracula_config.txt And, before it would process, but then I was looking into SLURMS and somehow misconfigured it. Now I get: I tried to reconfig the file and got it running again, but still get the error: ----------------------------------------------------------------------------------- (base) danielsalinas@danielsalinas-linux:~$ 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 ----------------------------------------------------------------------------------- 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
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