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BCL2FASTQ2 Pipeline Errors

I am trying to run the bcl2fastq2 pipeline on my BCL files to convert them to FastQ files. When I do this with the latest version of the bcl2fastq2 module on my cluster (bcl2fastq2/2-20-0-foss-2016a), it creates the files according to the sample names in the sample sheet, however after doing this, the process stops because of a bunch of these errors happening in different threads

ERROR: Thread: 5 caught an exception first: Dynamic exception type: std::bad_alloc
std::exception::what: std::bad_alloc

This data has been previously worked on and this error did not occur (as far as I know), so I was wondering how I can about debugging this.

rna-seq fastq bcl illumina
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updated by finswimmer finswimmer • written by fouerghi20 • fouerghi20

How much memory are you allocating for your job? I suggest you in crease that and try again. You may also want to reduce the number of worker (read/write) threads if you are assigning a lot of them.

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written by GenoMax GenoMax

How can I go about reducing the number of worker threads?

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written by fouerghi20 • fouerghi20

Change these options for your bcl2fastq command line :

-r [ --loading-threads ] arg (=4)               number of threads used for loading BCL data
-w [ --writing-threads ] arg (=4)               number of threads used for writing FASTQ data.
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written by GenoMax GenoMax

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