WorkflowError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/Snakefile, line 7: Config file must be given as JSON or YAML with keys at top level.

[VAMMGA]

[VAMMGA]

I am a beginner of HippUnfold, I met some problems in the use and have not been effectively solved, I downloaded the container version of HippUnfold and wrote a script to run different tasks. However, during the running process, I found that running 50 tasks would fail 1 or 2 tasks, running the 1 or 2 tasks alone is no problem. However, I adjusted different tasks by using different calculation directories and output directories, but the situation still exists, and the errors are not the same. The multi-test experiment test did not find an effective solution. I would appreciate it if you could help me to have a look. I am still looking forward to your reply. 【error1】 INFO: Converting SIF file to temporary sandbox... WorkflowError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/Snakefile, line 7: Config file must be given as JSON or YAML with keys at top level. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/Snakefile", line 7, in INFO: Cleaning up image...

other error:

It can be confirmed that there is no problem in the calculation examples, and errors will be reported in separate calculation. It is not clear what content conflicts lead to abnormal operation and different errors will appear. I often get this error when I try to split the calculation between different directories.

【error2】 [Mon May 20 16:08:07 2024] Error in rule cp_template_to_unfold: jobid: 124 input: /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-1mm_midthickness.surf.gii output: work/sub-N0013/ses-N00131/surf/sub-N0013_ses-N00131_hemi-R_space-unfold_den-1mm_label-hipp_midthickness.surf.gii shell: cp /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/../resources/unfold_template_hipp/tpl-avg_space-unfold_den-1mm_midthickness.surf.gii work/sub-N0013/ses-N00131/surf/sub-N0013_ses-N00131_hemi-R_space-unfold_den-1mm_label-hipp_midthickness.surf.gii && wb_command -set-structure work/sub-N0013/ses-N00131/surf/sub-N0013_ses-N00131_hemi-R_space-unfold_den-1mm_label-hipp_midthickness.surf.gii CORTEX_RIGHT -surface-type FLAT -surface-secondary-type MIDTHICKNESS (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) 【other errors】

【Sub.sh script】 #!/bin/bash #SBATCH -p v6_384 #SBATCH -N 1 #SBATCH -n 64 #SBATCH --exclusive

module load singularity/3.9.9 module load anaconda/3.7.3-zyq export PATH=/public1/wshome/ws221/sch0205/xumf/sci0048/install/bin:$PATH export Brain_dir=/public1/wshome/ws221/sch0205/xumf/sci0048/BNU_HY_CBIRD export out_dir=/public1/wshome/ws221/sch0205/xumf/sci0048/test1/output_BNU_HY_CBIRD export tool_dir=/public1/wshome/ws221/sch0205/xumf/sci0048 start_time=$(date +%s) mkdir ${out_dir} doit() { Subj_id="${1}" if [ ! -f ${out_dir}/work/sub-${Subj_id}_work.tar.gz ]; then rm -r ${out_dir}/work/sub-${Subj_id} rm -r ${out_dir}/hippunfold/sub-${Subj_id} echo "Processing ${Subj_id}" singularity run --bind ${Brain_dir}:/bids,${out_dir}:/output -e ${tool_dir}/khanlab_hippunfold_latest.sif /bids /output participant --modality T1w --cores 64 --participant-label ${Subj_id} --output-density 1mm Fi export -f doit Listfile=${1} cat ${Listfile} |parallel -j 5 --tmpdir /public1/wshome/ws221/sch0205/xumf/sci0048/tmp doit end_time=$(date +%s) echo "It took $(($end_time - $start_time)) seconds for the seg of hipp..."

【Subm_jobs.sh script】 #!/bin/bash job_info_file="job_info.txt" rm -f "$job_info_file" touch "$job_info_file" sublist_dir=/public1/wshome/ws221/sch0205/xumf/sci0048/sublist_BNU_HY_CBIRD maxjobs=5 i=1 #新的任务需要从1开始 while (( ${i} < 3 )); do #总人数除以5，向上取整+1 JobN=$(squeue -u sci0048 | grep -c " R ") if [ "$JobN" -lt "$maxjobs" ]; then echo "正在运行的作业数量 ($JobN) 小于 $maxjobs，可以提交新作业。" Listfile=${sublist_dir}/Subjlist_${i} # rm -f ${Listfile} Start=$[i_5-4] Stop=$[i_5] sed -n "${Start},${Stop}p" ${sublist_dir}/Subjlist_all_BX >> ${Listfile} #需要修改，保留最后一行的回车 timestamp=$(date +%Y-%m-%d\ %H:%M:%S) job_id=$(sbatch sub.sh ${Listfile}| awk '{print $NF}') echo "Submitted job $job_id at $timestamp" echo "JobID: $job_id, Submission Time: $timestamp" >> "$job_info_file" i=$[i+1] fi sleep 20 done echo "All jobs submitted."