no output for methylationExtractor

seems removeduplicate component generates a truncated bam fil : `Summarising genome-wide cytosine methylation report parameters:

Generating comprehensive genome-wide cytosine report (output format: ) Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files Using zero-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined) Genome folder was specified as /work/ng6-test/jflow_gsalin/work/methylseq/wf000069/BismarkGenomePreparation_default/

Checking file >>/work/ng6-test/jflow_gsalin/work/methylseq/wf000069/RemoveDuplicate_paired/Histone-1-3_clean.bam<< for signs of file truncation... Captured error message: '[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes'

[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting... ` and then, no data loaded in the database