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problems using provenance during upload

Description

Using Synapse Client 1.4.dev1.

synapse add /ycga-ba/ba_sequencers3/scratch/gc223/data/PsychENCODE/Mapped/Sample_11_015/accepted_hits.bam --parentid syn5934231 --name 11_015.bam --used http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit --executed /ycga-ba/ba_sequencers3/scratch/gc223/data/PsychENCODE/Mapped/script.sh --annotations '{"consortium": "PEC", "grant": "U01MH103365", "group": "Yale", "PI": "Flora vaccarino", "study": "iPSC", "disease": "Control", "organism": "Homo Sapiens", "lifeStage": "Fetal", "organ": "NA", "tissueType": "Organoids", "tissueTypeAbrv": "ORG", "CellType": "NeuN-", "treatmentType": "control", "dataType": "total", "dataSubType": "NA", "assay": "RNA-seq", "assayTarget": "NA", "libraryPrep": "rRNA depletion", "runType": "paired-end", "readLength": "75", "platform": "HiSeq2000", "fileType": "bam", "accessControl": "Embargo"}'

as a result I get then following error:
SynapseFileNotFoundError: File /ycga-ba/ba_sequencers3/scratch/gc223/data/PsychENCODE/Mapped/script.sh not found in Synapse

needless to say that the file script.sh is under the path specified.

Environment

Status

Assignee

Larsson Omberg

Reporter

Kristen Dang

Validator

Kristen Dang

Components

Fix versions

Affects versions

py-1.5

Priority

Major