eu_report_fastq_content_errors

Finds FASTQ files with a content error and indicates the error.

Given an input file containing experiment identifiers, one per row, looks up all FASTQ files on the experiment to check for content errors. If any FASTQ file object has a status property of “content_error”, then the content error message will be extracted from the property content_error_detail. A new file will be output containing the error details.

usage: report_fastq_content_errors.py [-h] [-m DCC_MODE] -i INFILE -o OUTFILE

Named Arguments

-m, --dcc-mode
The ENCODE Portal site (‘prod’ or ‘dev’, or an explicit host name, i.e. ‘demo.encodedcc.org’) to connect to.
-i, --infile
Input file containing experiment identifiers, one per row. Any line starting with a ‘#’ will be skipped.
-o, --outfile

Output file containing three tab-delimited columns for each FASTQ file that is reported:

  1. The accession of the Experiment record that the FASTQ file record belongs to.
  2. The accession of the FASTQ file record.
  3. The error message stored in the File objects content_error_detail property.