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bigbio / sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files
Apache License 2.0
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technical replicates are wrongly handle. #80

Closed ypriverol closed 3 years ago

ypriverol commented 3 years ago

The export to OpenMS with technical replicates is wrongly handled.

ypriverol commented 3 years ago

https://github.com/multiomics/multiomics-configs/blob/master/datasets/cancer-celllines-samples/sample-specific/PXD012255-Sample-1.tsv

ypriverol commented 3 years ago

Error in the pipeline: 

File '/homes/yperez/.OpenMS/OpenMS.ini' is deprecated.
Updating missing/wrong entries in '/homes/yperez/.OpenMS/OpenMS.ini' with defaults!
Default-Parameter 'temp_dir' overridden: '' --> '/hps/nobackup2/proteomics/yperez_temp/temp/'!
Error: Unexpected internal error ((Fraction Group, Fraction, Label) combination can only appear once)

The OpenMS result: 

Fraction_Group  Fraction    Spectra_Filepath    Label   Sample
1   1   Phospho_redissolve_final_01.mzML    1   1
1   1   Phospho_redissolve_final_02.mzML    1   1
1   1   Phospho_redissolve_final_03.mzML    1   1
1   1   Phospho_redissolve_final_04.mzML    1   1
1   1   Phospho_redissolve_final_05.mzML    1   1
1   1   Phospho_redissolve_final_06.mzML    1   1
1   1   Phospho_redissolve_final_07.mzML    1   1
1   1   Phospho_redissolve_final_08.mzML    1   1
1   1   Phospho_redissolve_final_09.mzML    1   1
1   1   Phospho_redissolve_final_10.mzML    1   1
1   1   Phospho_redissolve_final_11.mzML    1   1
1   1   Phospho_redissolve_final_12.mzML    1   1
1   1   Phospho_redissolve_final_13.mzML    1   1
1   1   Phospho_redissolve_final_14.mzML    1   1
1   1   Phospho_redissolve_final_15.mzML    1   1
1   1   Phospho_redissolve_final_16.mzML    1   1
1   1   Phospho_redissolve_final_17.mzML    1   1
1   1   Phospho_redissolve_final_18.mzML    1   1
1   1   Phospho_redissolve_final_19.mzML    1   1
1   1   Phospho_redissolve_final_20.mzML    1   1
1   1   Phospho_redissolve_final_21.mzML    1   1
1   1   Phospho_redissolve_final_22.mzML    1   1
1   1   Phospho_redissolve_final_23.mzML    1   1
1   1   Phospho_redissolve_final_24.mzML    1   1
1   1   Phospho_redissolve_final_25.mzML    1   1
1   1   Phospho_redissolve_final_26.mzML    1   1
1   1   Phospho_redissolve_final_27.mzML    1   1
1   1   Phospho_redissolve_final_28.mzML    1   1
1   1   Phospho_redissolve_final_29.mzML    1   1
1   1   Phospho_redissolve_final_30.mzML    1   1
1   1   Phospho_redissolve_final_31.mzML    1   1
1   1   Phospho_redissolve_final_32.mzML    1   1
1   1   Phospho_redissolve_final_33.mzML    1   1
1   1   Phospho_redissolve_final_34.mzML    1   1
1   1   Phospho_redissolve_final_35.mzML    1   1
1   1   Phospho_redissolve_final_36.mzML    1   1
1   1   Phospho_redissolve_final_37.mzML    1   1
1   1   Phospho_redissolve_final_38.mzML    1   1
1   1   Phospho_redissolve_final_39.mzML    1   1
1   1   Phospho_redissolve_final_40.mzML    1   1

Sample  MSstats_Condition   MSstats_BioReplicate
1   Homo sapiens|colon|HCT 116|not available|not available|colon carcinoma|not available|not available|not available|not available  1
jpfeuffer commented 3 years ago

Is this still relevant? I think there was an error in the SDRF?