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broadinstitute / gdctools

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons
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gdc_report should tolerate missing filter file #84

Open noblem opened 6 years ago

noblem commented 6 years ago

From 2018_08_02 nightly ingest:

Error in file(file, "rt") : cannot open the connection
2018-08-02 01:53:45,795[INFO]: Calls: main -> getFilterTable -> read.table -> file
2018-08-02 01:53:45,795[INFO]: In addition: Warning message:
2018-08-02 01:53:45,795[INFO]: In file(file, "rt") :
2018-08-02 01:53:45,795[INFO]:   cannot open file '/xchip/gdac_data/gdc/sample_reports/report_2018_08_02/TCGA.filte
red_samples.txt': No such file or directory
2018-08-02 01:53:45,795[INFO]: 4: file(file, "rt")
2018-08-02 01:53:45,795[INFO]: 3: read.table(filtered.file, sep = "\t", header = TRUE, stringsAsFactors = FALSE)
2018-08-02 01:53:45,796[INFO]: 2: getFilterTable(reportDir, datestamp, aggregateNametoTumorTypesMap)
2018-08-02 01:53:45,796[INFO]: 1: main(commandArgs(trailingOnly = TRUE))