From 9c2c74e2935ef9d68f993c5072d5802856b8c1b4 Mon Sep 17 00:00:00 2001 From: "Amanda Wadams {amanda.wadams@uconn.edu}" Date: Mon, 24 Feb 2020 07:54:47 -0500 Subject: [PATCH] first submission --- bids/README | 5 +++ bids/code/bidscoin/bidscoiner.errors | 0 bids/code/bidscoin/bidscoiner.log | 6 ++++ .../bidscoin/samples/anat/FLAIR/.placeholder | 0 .../bidscoin/samples/anat/FLASH/.placeholder | 0 .../bidscoin/samples/anat/PD/.placeholder | 0 .../bidscoin/samples/anat/PDT2/.placeholder | 0 .../bidscoin/samples/anat/PDmap/.placeholder | 0 .../samples/anat/SWImagandphase/.placeholder | 0 .../bidscoin/samples/anat/T1map/.placeholder | 0 .../bidscoin/samples/anat/T1rho/.placeholder | 0 .../bidscoin/samples/anat/T1w/.placeholder | 0 .../bidscoin/samples/anat/T2map/.placeholder | 0 .../bidscoin/samples/anat/T2star/.placeholder | 0 .../bidscoin/samples/anat/T2w/.placeholder | 0 .../bidscoin/samples/anat/angio/.placeholder | 0 .../samples/anat/defacemask/.placeholder | 0 .../samples/anat/inplaneT1/.placeholder | 0 .../samples/anat/inplaneT2/.placeholder | 0 bids/code/bidscoin/samples/beh/.placeholder | 0 .../bidscoin/samples/dwi/dwi/.placeholder | 0 .../bidscoin/samples/dwi/sbref/.placeholder | 0 .../bidscoin/samples/fmap/epi/.placeholder | 0 .../samples/fmap/fieldmap/.placeholder | 0 .../samples/fmap/magnitude/.placeholder | 0 .../samples/fmap/magnitude1/.placeholder | 0 .../samples/fmap/magnitude2/.placeholder | 0 .../bidscoin/samples/fmap/phase1/.placeholder | 0 .../bidscoin/samples/fmap/phase2/.placeholder | 0 .../samples/fmap/phasediff/.placeholder | 0 .../bidscoin/samples/func/bold/.placeholder | 0 .../bidscoin/samples/func/events/.placeholder | 0 .../bidscoin/samples/func/physio/.placeholder | 0 .../bidscoin/samples/func/sbref/.placeholder | 0 .../bidscoin/samples/func/stim/.placeholder | 0 .../bidscoin/samples/pet/pet/.placeholder | 0 bids/code/sbatch_step1a.sh | 2 +- bids/code/sbatch_step1b.sh | 2 +- bids/code/sbatch_step2.sh | 4 +-- bids/code/sbatch_step3.sh | 2 +- bids/code/slurm-3092069.out | 1 + bids/code/step1a_error_3092133_4294967294.log | 6 ++++ .../code/step1a_output_3092133_4294967294.log | 2 ++ bids/code/step1b_error_3092135_4294967294.log | 36 +++++++++++++++++++ .../code/step1b_output_3092135_4294967294.log | 28 +++++++++++++++ bids/code/step2_error_3096308_4294967294.log | 12 +++++++ bids/code/step2_output_3096308_4294967294.log | 0 bids/code/step3_error_3096318_4294967294.log | 24 +++++++++++++ bids/code/step3_output_3096318_4294967294.log | 0 bidscoiner/bids/code/reorganize.sh | 9 +++++ bidscoiner/bids/code/sbatch_step1.sh | 29 +++++++++++++++ bidscoiner/bids/code/sbatch_step2.sh | 29 +++++++++++++++ bidscoiner/bids/code/sbatch_step3.sh | 22 ++++++++++++ step1a_error_3091907_4294967294.log | 6 ++++ step1a_error_3091921_4294967294.log | 10 ++++++ step1a_error_3092046_4294967294.log | 10 ++++++ step1a_output_3091907_4294967294.log | 2 ++ step1a_output_3091921_4294967294.log | 0 step1a_output_3092046_4294967294.log | 0 step1b_error_3091908_4294967294.log | 22 ++++++++++++ step1b_error_3091922_4294967294.log | 22 ++++++++++++ step1b_error_3092048_4294967294.log | 22 ++++++++++++ step1b_error_3092062_4294967294.log | 22 ++++++++++++ step1b_output_3091908_4294967294.log | 0 step1b_output_3091922_4294967294.log | 0 step1b_output_3092048_4294967294.log | 0 step1b_output_3092062_4294967294.log | 0 67 files changed, 330 insertions(+), 5 deletions(-) create mode 100644 bids/README create mode 100644 bids/code/bidscoin/bidscoiner.errors create mode 100644 bids/code/bidscoin/bidscoiner.log create mode 100644 bids/code/bidscoin/samples/anat/FLAIR/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/FLASH/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/PD/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/PDT2/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/PDmap/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/SWImagandphase/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T1map/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T1rho/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T1w/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T2map/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T2star/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/T2w/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/angio/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/defacemask/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/inplaneT1/.placeholder create mode 100644 bids/code/bidscoin/samples/anat/inplaneT2/.placeholder create mode 100644 bids/code/bidscoin/samples/beh/.placeholder create mode 100644 bids/code/bidscoin/samples/dwi/dwi/.placeholder create mode 100644 bids/code/bidscoin/samples/dwi/sbref/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/epi/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/fieldmap/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/magnitude/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/magnitude1/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/magnitude2/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/phase1/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/phase2/.placeholder create mode 100644 bids/code/bidscoin/samples/fmap/phasediff/.placeholder create mode 100644 bids/code/bidscoin/samples/func/bold/.placeholder create mode 100644 bids/code/bidscoin/samples/func/events/.placeholder create mode 100644 bids/code/bidscoin/samples/func/physio/.placeholder create mode 100644 bids/code/bidscoin/samples/func/sbref/.placeholder create mode 100644 bids/code/bidscoin/samples/func/stim/.placeholder create mode 100644 bids/code/bidscoin/samples/pet/pet/.placeholder create mode 100644 bids/code/slurm-3092069.out create mode 100644 bids/code/step1a_error_3092133_4294967294.log create mode 100644 bids/code/step1a_output_3092133_4294967294.log create mode 100644 bids/code/step1b_error_3092135_4294967294.log create mode 100644 bids/code/step1b_output_3092135_4294967294.log create mode 100644 bids/code/step2_error_3096308_4294967294.log create mode 100644 bids/code/step2_output_3096308_4294967294.log create mode 100644 bids/code/step3_error_3096318_4294967294.log create mode 100644 bids/code/step3_output_3096318_4294967294.log create mode 100755 bidscoiner/bids/code/reorganize.sh create mode 100755 bidscoiner/bids/code/sbatch_step1.sh create mode 100755 bidscoiner/bids/code/sbatch_step2.sh create mode 100755 bidscoiner/bids/code/sbatch_step3.sh create mode 100644 step1a_error_3091907_4294967294.log create mode 100644 step1a_error_3091921_4294967294.log create mode 100644 step1a_error_3092046_4294967294.log create mode 100644 step1a_output_3091907_4294967294.log create mode 100644 step1a_output_3091921_4294967294.log create mode 100644 step1a_output_3092046_4294967294.log create mode 100644 step1b_error_3091908_4294967294.log create mode 100644 step1b_error_3091922_4294967294.log create mode 100644 step1b_error_3092048_4294967294.log create mode 100644 step1b_error_3092062_4294967294.log create mode 100644 step1b_output_3091908_4294967294.log create mode 100644 step1b_output_3091922_4294967294.log create mode 100644 step1b_output_3092048_4294967294.log create mode 100644 step1b_output_3092062_4294967294.log diff --git a/bids/README b/bids/README new file mode 100644 index 0000000..bb178da --- /dev/null +++ b/bids/README @@ -0,0 +1,5 @@ +A free form text ( README ) describing the dataset in more details that SHOULD be provided + +The raw BIDS data was created using BIDScoin 2.3 +All provenance information and settings can be found in ./code/bidscoin +For more information see: https://github.com/Donders-Institute/bidscoin \ No newline at end of file diff --git a/bids/code/bidscoin/bidscoiner.errors b/bids/code/bidscoin/bidscoiner.errors new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/bidscoiner.log b/bids/code/bidscoin/bidscoiner.log new file mode 100644 index 0000000..8cacc5e --- /dev/null +++ b/bids/code/bidscoin/bidscoiner.log @@ -0,0 +1,6 @@ +2020-02-23 11:31:26 - bidscoin - INFO +2020-02-23 11:31:26 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-23 11:31:26 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-23 11:31:26 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json +2020-02-23 11:31:26 - bidscoin - INFO Creating README file: /data/bids/README +2020-02-23 11:31:26 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml diff --git a/bids/code/bidscoin/samples/anat/FLAIR/.placeholder b/bids/code/bidscoin/samples/anat/FLAIR/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/FLASH/.placeholder b/bids/code/bidscoin/samples/anat/FLASH/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/PD/.placeholder b/bids/code/bidscoin/samples/anat/PD/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/PDT2/.placeholder b/bids/code/bidscoin/samples/anat/PDT2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/PDmap/.placeholder b/bids/code/bidscoin/samples/anat/PDmap/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/SWImagandphase/.placeholder b/bids/code/bidscoin/samples/anat/SWImagandphase/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T1map/.placeholder b/bids/code/bidscoin/samples/anat/T1map/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T1rho/.placeholder b/bids/code/bidscoin/samples/anat/T1rho/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T1w/.placeholder b/bids/code/bidscoin/samples/anat/T1w/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T2map/.placeholder b/bids/code/bidscoin/samples/anat/T2map/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T2star/.placeholder b/bids/code/bidscoin/samples/anat/T2star/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/T2w/.placeholder b/bids/code/bidscoin/samples/anat/T2w/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/angio/.placeholder b/bids/code/bidscoin/samples/anat/angio/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/defacemask/.placeholder b/bids/code/bidscoin/samples/anat/defacemask/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/inplaneT1/.placeholder b/bids/code/bidscoin/samples/anat/inplaneT1/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/anat/inplaneT2/.placeholder b/bids/code/bidscoin/samples/anat/inplaneT2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/beh/.placeholder b/bids/code/bidscoin/samples/beh/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/dwi/dwi/.placeholder b/bids/code/bidscoin/samples/dwi/dwi/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/dwi/sbref/.placeholder b/bids/code/bidscoin/samples/dwi/sbref/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/epi/.placeholder b/bids/code/bidscoin/samples/fmap/epi/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/fieldmap/.placeholder b/bids/code/bidscoin/samples/fmap/fieldmap/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/magnitude/.placeholder b/bids/code/bidscoin/samples/fmap/magnitude/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/magnitude1/.placeholder b/bids/code/bidscoin/samples/fmap/magnitude1/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/magnitude2/.placeholder b/bids/code/bidscoin/samples/fmap/magnitude2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/phase1/.placeholder b/bids/code/bidscoin/samples/fmap/phase1/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/phase2/.placeholder b/bids/code/bidscoin/samples/fmap/phase2/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/fmap/phasediff/.placeholder b/bids/code/bidscoin/samples/fmap/phasediff/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/func/bold/.placeholder b/bids/code/bidscoin/samples/func/bold/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/func/events/.placeholder b/bids/code/bidscoin/samples/func/events/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/func/physio/.placeholder b/bids/code/bidscoin/samples/func/physio/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/func/sbref/.placeholder b/bids/code/bidscoin/samples/func/sbref/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/func/stim/.placeholder b/bids/code/bidscoin/samples/func/stim/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/samples/pet/pet/.placeholder b/bids/code/bidscoin/samples/pet/pet/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/sbatch_step1a.sh b/bids/code/sbatch_step1a.sh index d6a31be..ca39ee5 100755 --- a/bids/code/sbatch_step1a.sh +++ b/bids/code/sbatch_step1a.sh @@ -16,7 +16,7 @@ module load singularity ##### run container commands # create samples under bids/code/bidscoiner -singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \ +singularity run --bind /scratch/amw17004/hw2:/data \ /scratch/psyc5171/containers/birc-bids_latest.sif \ bidstrainer.py /data/bids diff --git a/bids/code/sbatch_step1b.sh b/bids/code/sbatch_step1b.sh index 40aaf7e..f9b6596 100755 --- a/bids/code/sbatch_step1b.sh +++ b/bids/code/sbatch_step1b.sh @@ -17,7 +17,7 @@ module load singularity # reorganize the files -singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \ +singularity run --bind /scratch/amw17004/hw2:/data \ /scratch/psyc5171/containers/birc-bids_latest.sif \ /data/bids/code/reorganize.sh diff --git a/bids/code/sbatch_step2.sh b/bids/code/sbatch_step2.sh index 455bb2c..2adebc9 100755 --- a/bids/code/sbatch_step2.sh +++ b/bids/code/sbatch_step2.sh @@ -15,13 +15,13 @@ module load singularity ##### run container commands # training on the sample data -singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ +singularity run --bind /scratch/psyc5171/amw17004/bidscoiner:/data \ /scratch/psyc5171/containers/birc-bids_latest.sif \ bidstrainer.py /data/bids # Create the bidsmap -singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ +singularity run --bind /scratch/psyc5171/amw17004/hw2:/data \ /scratch/psyc5171/containers/birc-bids_latest.sif \ bidsmapper.py -t /data/bids/code/bidscoin/bidsmap_sample.yaml \ -i 0 /data/raw /data/bids diff --git a/bids/code/sbatch_step3.sh b/bids/code/sbatch_step3.sh index ae2a84c..518cba2 100755 --- a/bids/code/sbatch_step3.sh +++ b/bids/code/sbatch_step3.sh @@ -15,7 +15,7 @@ module load singularity ##### run container commands # Run bidscoiner to convert the raw data to BIDSa -singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ +singularity run --bind /scratch/amw17004/hw2:/data \ /scratch/psyc5171/containers/birc-bids_latest.sif \ bidscoiner.py -f /data/raw /data/bids diff --git a/bids/code/slurm-3092069.out b/bids/code/slurm-3092069.out new file mode 100644 index 0000000..f5ce204 --- /dev/null +++ b/bids/code/slurm-3092069.out @@ -0,0 +1 @@ +ls: cannot access /data/raw/sub-*: No such file or directory diff --git a/bids/code/step1a_error_3092133_4294967294.log b/bids/code/step1a_error_3092133_4294967294.log new file mode 100644 index 0000000..6eae0fd --- /dev/null +++ b/bids/code/step1a_error_3092133_4294967294.log @@ -0,0 +1,6 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/bids/code/step1a_output_3092133_4294967294.log b/bids/code/step1a_output_3092133_4294967294.log new file mode 100644 index 0000000..d1402b2 --- /dev/null +++ b/bids/code/step1a_output_3092133_4294967294.log @@ -0,0 +1,2 @@ +Creating an empty samples directory tree: /data/bids/code/bidscoin/samples +Fill the directory tree with example DICOM files and re-run bidstrainer.py diff --git a/bids/code/step1b_error_3092135_4294967294.log b/bids/code/step1b_error_3092135_4294967294.log new file mode 100644 index 0000000..41a034e --- /dev/null +++ b/bids/code/step1b_error_3092135_4294967294.log @@ -0,0 +1,36 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +/data/bids/code/reorganize.sh: line 9: m: command not found diff --git a/bids/code/step1b_output_3092135_4294967294.log b/bids/code/step1b_output_3092135_4294967294.log new file mode 100644 index 0000000..2e3834b --- /dev/null +++ b/bids/code/step1b_output_3092135_4294967294.log @@ -0,0 +1,28 @@ +>> Processing: /data/raw/sub-TD902TD/1 (128 files) + Creating: /data/raw/sub-TD902TD/1/001-AAHead_Scout +>> Processing: /data/raw/sub-TD902TD/10 (13 files) + Creating: /data/raw/sub-TD902TD/10/010-task-prosody +>> Processing: /data/raw/sub-TD902TD/11 (1 files) + Creating: /data/raw/sub-TD902TD/11/011-task-prosody_PhysioLog +>> Processing: /data/raw/sub-TD902TD/12 (1 files) + Creating: /data/raw/sub-TD902TD/12/012-task-prosody_SBRef +>> Processing: /data/raw/sub-TD902TD/13 (336 files) + Creating: /data/raw/sub-TD902TD/13/013-task-prosody +>> Processing: /data/raw/sub-TD902TD/14 (1 files) + Creating: /data/raw/sub-TD902TD/14/014-task-prosody_PhysioLog +>> Processing: /data/raw/sub-TD902TD/2 (5 files) + Creating: /data/raw/sub-TD902TD/2/002-AAHead_Scout_MPR_sag +>> Processing: /data/raw/sub-TD902TD/3 (3 files) + Creating: /data/raw/sub-TD902TD/3/003-AAHead_Scout_MPR_cor +>> Processing: /data/raw/sub-TD902TD/4 (3 files) + Creating: /data/raw/sub-TD902TD/4/004-AAHead_Scout_MPR_tra +>> Processing: /data/raw/sub-TD902TD/5 (176 files) + Creating: /data/raw/sub-TD902TD/5/005-T1w +>> Processing: /data/raw/sub-TD902TD/6 (1 files) + Creating: /data/raw/sub-TD902TD/6/006-task-music_SBRef +>> Processing: /data/raw/sub-TD902TD/7 (287 files) + Creating: /data/raw/sub-TD902TD/7/007-task-music +>> Processing: /data/raw/sub-TD902TD/8 (1 files) + Creating: /data/raw/sub-TD902TD/8/008-task-music_PhysioLog +>> Processing: /data/raw/sub-TD902TD/9 (1 files) + Creating: /data/raw/sub-TD902TD/9/009-task-prosody_SBRef diff --git a/bids/code/step2_error_3096308_4294967294.log b/bids/code/step2_error_3096308_4294967294.log new file mode 100644 index 0000000..51b7584 --- /dev/null +++ b/bids/code/step2_error_3096308_4294967294.log @@ -0,0 +1,12 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +2020-02-23 11:27:33 - bidscoin - INFO ------------ START BIDStrainer ------------ +2020-02-23 11:27:33 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml +2020-02-23 11:27:33 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-23 11:27:33 - bidscoin - INFO ------------ FINISHED! ------------ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +FATAL:  container creation failed: mount /scratch/psyc5171/amw17004/hw2->/data error: while mounting /scratch/psyc5171/amw17004/hw2: mount source /scratch/psyc5171/amw17004/hw2 doesn't exist diff --git a/bids/code/step2_output_3096308_4294967294.log b/bids/code/step2_output_3096308_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/step3_error_3096318_4294967294.log b/bids/code/step3_error_3096318_4294967294.log new file mode 100644 index 0000000..716254e --- /dev/null +++ b/bids/code/step3_error_3096318_4294967294.log @@ -0,0 +1,24 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +2020-02-23 11:31:26 - bidscoin - INFO +2020-02-23 11:31:26 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-23 11:31:26 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-23 11:31:26 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json +2020-02-23 11:31:26 - bidscoin - INFO Creating README file: /data/bids/README +2020-02-23 11:31:26 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml +Traceback (most recent call last): + File "/usr/local/miniconda/bin/bidscoiner.py", line 4, in + __import__('pkg_resources').run_script('bidscoin==2.3', 'bidscoiner.py') + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script + self.require(requires)[0].run_script(script_name, ns) + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script + exec(code, namespace, namespace) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/bidscoiner.py", line 569, in + sesprefix = args.sesprefix) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/bidscoiner.py", line 436, in bidscoiner + bidsignore_items = [item.strip() for item in bidsmap['Options']['bidscoin']['bidsignore'].split(';')] +KeyError: 'Options' diff --git a/bids/code/step3_output_3096318_4294967294.log b/bids/code/step3_output_3096318_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/bidscoiner/bids/code/reorganize.sh b/bidscoiner/bids/code/reorganize.sh new file mode 100755 index 0000000..5a96871 --- /dev/null +++ b/bidscoiner/bids/code/reorganize.sh @@ -0,0 +1,9 @@ +#!/bin/bash +# rename DICOM folders to help bidsmap +SUBJECT=$1 +for d in /data/raw/sub-${SUBJECT}/*; do + dicomsort.py -r -e .dcm $d +done + +mv /data/raw/sub-${SUBJECT}/*/* /data/raw/sub-${SUBJECT} +rm -rf /data/raw/sub-${SUBJECT}/[1-9]* diff --git a/bidscoiner/bids/code/sbatch_step1.sh b/bidscoiner/bids/code/sbatch_step1.sh new file mode 100755 index 0000000..e1052d7 --- /dev/null +++ b/bidscoiner/bids/code/sbatch_step1.sh @@ -0,0 +1,29 @@ +#!/bin/bash +##### Job definition +# TODO: Edit email address below +#SBATCH --nodes=1 # OpenMP requires a single node +#SBATCH --ntasks=1 # Run a single serial task +#SBATCH --time=00:10:00 # Time limit hh:mm:ss +#SBATCH -e step1_error_%A_%a.log # Standard error +#SBATCH -o step1_output_%A_%a.log # Standard output +#SBATCH --job-name=bidssetup # Descriptive job name +#SBATCH --partition=serial + +##### load required modules + +module load singularity + +##### run container commands + +# create samples under bids/code/bidscoiner +singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \ + /scratch/psyc5171/containers/birc-bids_latest.sif \ + bidstrainer.py /data/bids + + +# reorganize the files +singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \ + /scratch/psyc5171/containers/birc-bids_latest.sif \ + /data/bids/code/reorganize.sh IBRAIN002 + + diff --git a/bidscoiner/bids/code/sbatch_step2.sh b/bidscoiner/bids/code/sbatch_step2.sh new file mode 100755 index 0000000..0dd90c1 --- /dev/null +++ b/bidscoiner/bids/code/sbatch_step2.sh @@ -0,0 +1,29 @@ +#!/bin/bash +##### Job definition +#SBATCH --nodes=1 # OpenMP requires a single node +#SBATCH --ntasks=1 # Run a single serial task +#SBATCH --time=00:10:00 # Time limit hh:mm:ss +#SBATCH -e step2_error_%A_%a.log # Standard error +#SBATCH -o step2_output_%A_%a.log # Standard output +#SBATCH --job-name=bidstrain # Descriptive job name +#SBATCH --partition=serial + +##### load required modules + +module load singularity + +##### run container commands + +# training on the sample data +singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ + /scratch/psyc5171/containers/birc-bids_latest.sif \ + bidstrainer.py /data/bids + + +# Create the bidsmap +singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ + /scratch/psyc5171/containers/birc-bids_latest.sif \ + bidsmapper.py -t /data/bids/code/bidscoin/bidsmap_sample.yaml \ + -i 0 /data/raw /data/bids + + diff --git a/bidscoiner/bids/code/sbatch_step3.sh b/bidscoiner/bids/code/sbatch_step3.sh new file mode 100755 index 0000000..ae2a84c --- /dev/null +++ b/bidscoiner/bids/code/sbatch_step3.sh @@ -0,0 +1,22 @@ +#!/bin/bash +##### Job definition +#SBATCH --nodes=1 # OpenMP requires a single node +#SBATCH --ntasks=1 # Run a single serial task +#SBATCH --time=00:10:00 # Time limit hh:mm:ss +#SBATCH -e step3_error_%A_%a.log # Standard error +#SBATCH -o step3_output_%A_%a.log # Standard output +#SBATCH --job-name=bidscoin # Descriptive job name +#SBATCH --partition=serial + +##### load required modules + +module load singularity + +##### run container commands + +# Run bidscoiner to convert the raw data to BIDSa +singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \ + /scratch/psyc5171/containers/birc-bids_latest.sif \ + bidscoiner.py -f /data/raw /data/bids + + diff --git a/step1a_error_3091907_4294967294.log b/step1a_error_3091907_4294967294.log new file mode 100644 index 0000000..6eae0fd --- /dev/null +++ b/step1a_error_3091907_4294967294.log @@ -0,0 +1,6 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/step1a_error_3091921_4294967294.log b/step1a_error_3091921_4294967294.log new file mode 100644 index 0000000..cfa968f --- /dev/null +++ b/step1a_error_3091921_4294967294.log @@ -0,0 +1,10 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +2020-02-20 08:05:21 - bidscoin - INFO ------------ START BIDStrainer ------------ +2020-02-20 08:05:21 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml +2020-02-20 08:05:21 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-20 08:05:21 - bidscoin - INFO ------------ FINISHED! ------------ diff --git a/step1a_error_3092046_4294967294.log b/step1a_error_3092046_4294967294.log new file mode 100644 index 0000000..4576a31 --- /dev/null +++ b/step1a_error_3092046_4294967294.log @@ -0,0 +1,10 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +2020-02-20 10:55:36 - bidscoin - INFO ------------ START BIDStrainer ------------ +2020-02-20 10:55:36 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml +2020-02-20 10:55:36 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-20 10:55:37 - bidscoin - INFO ------------ FINISHED! ------------ diff --git a/step1a_output_3091907_4294967294.log b/step1a_output_3091907_4294967294.log new file mode 100644 index 0000000..d1402b2 --- /dev/null +++ b/step1a_output_3091907_4294967294.log @@ -0,0 +1,2 @@ +Creating an empty samples directory tree: /data/bids/code/bidscoin/samples +Fill the directory tree with example DICOM files and re-run bidstrainer.py diff --git a/step1a_output_3091921_4294967294.log b/step1a_output_3091921_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/step1a_output_3092046_4294967294.log b/step1a_output_3092046_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/step1b_error_3091908_4294967294.log b/step1b_error_3091908_4294967294.log new file mode 100644 index 0000000..e61856b --- /dev/null +++ b/step1b_error_3091908_4294967294.log @@ -0,0 +1,22 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +Traceback (most recent call last): + File "/usr/local/miniconda/bin/dicomsort.py", line 4, in + __import__('pkg_resources').run_script('bidscoin==2.3', 'dicomsort.py') + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script + self.require(requires)[0].run_script(script_name, ns) + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script + exec(code, namespace, namespace) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 192, in + pattern = args.pattern) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 156, in sortsessions + dicomfiles = [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)] +FileNotFoundError: [Errno 2] No such file or directory: '/data/raw/sub-/*' +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +mv: cannot stat '/data/raw/sub-/*/*': No such file or directory +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/step1b_error_3091922_4294967294.log b/step1b_error_3091922_4294967294.log new file mode 100644 index 0000000..e61856b --- /dev/null +++ b/step1b_error_3091922_4294967294.log @@ -0,0 +1,22 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +Traceback (most recent call last): + File "/usr/local/miniconda/bin/dicomsort.py", line 4, in + __import__('pkg_resources').run_script('bidscoin==2.3', 'dicomsort.py') + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script + self.require(requires)[0].run_script(script_name, ns) + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script + exec(code, namespace, namespace) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 192, in + pattern = args.pattern) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 156, in sortsessions + dicomfiles = [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)] +FileNotFoundError: [Errno 2] No such file or directory: '/data/raw/sub-/*' +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +mv: cannot stat '/data/raw/sub-/*/*': No such file or directory +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/step1b_error_3092048_4294967294.log b/step1b_error_3092048_4294967294.log new file mode 100644 index 0000000..e61856b --- /dev/null +++ b/step1b_error_3092048_4294967294.log @@ -0,0 +1,22 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +Traceback (most recent call last): + File "/usr/local/miniconda/bin/dicomsort.py", line 4, in + __import__('pkg_resources').run_script('bidscoin==2.3', 'dicomsort.py') + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script + self.require(requires)[0].run_script(script_name, ns) + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script + exec(code, namespace, namespace) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 192, in + pattern = args.pattern) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 156, in sortsessions + dicomfiles = [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)] +FileNotFoundError: [Errno 2] No such file or directory: '/data/raw/sub-/*' +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +mv: cannot stat '/data/raw/sub-/*/*': No such file or directory +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/step1b_error_3092062_4294967294.log b/step1b_error_3092062_4294967294.log new file mode 100644 index 0000000..e61856b --- /dev/null +++ b/step1b_error_3092062_4294967294.log @@ -0,0 +1,22 @@ +WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +Traceback (most recent call last): + File "/usr/local/miniconda/bin/dicomsort.py", line 4, in + __import__('pkg_resources').run_script('bidscoin==2.3', 'dicomsort.py') + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script + self.require(requires)[0].run_script(script_name, ns) + File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script + exec(code, namespace, namespace) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 192, in + pattern = args.pattern) + File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/dicomsort.py", line 156, in sortsessions + dicomfiles = [os.path.join(sessionfolder,dcmfile) for dcmfile in os.listdir(sessionfolder) if re.match(pattern, dcmfile)] +FileNotFoundError: [Errno 2] No such file or directory: '/data/raw/sub-/*' +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. +mv: cannot stat '/data/raw/sub-/*/*': No such file or directory +ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. diff --git a/step1b_output_3091908_4294967294.log b/step1b_output_3091908_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/step1b_output_3091922_4294967294.log b/step1b_output_3091922_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/step1b_output_3092048_4294967294.log b/step1b_output_3092048_4294967294.log new file mode 100644 index 0000000..e69de29 diff --git a/step1b_output_3092062_4294967294.log b/step1b_output_3092062_4294967294.log new file mode 100644 index 0000000..e69de29