bcl2fastq errors during the software running
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8.7 years ago
Bnf83 ▴ 150

Hi guys, I'm trying to perform the bcl2fastq conversion of my .bcl files on cluster. Unfortunately, when running the sw, the following errors appear:

1: ERROR: Thread: 1 caught an exception first: Dynamic exception type: std::bad_alloc std::exception::what: std::bad_alloc

2: ERROR: Thread: 2 also caught an exception: Dynamic exception type: std::bad_alloc std::exception::what: std::bad_alloc

3: ERROR: Thread: 0 caught an exception first: Throw location unknown (consider using BOOST_THROW_EXCEPTION) Dynamic exception type: boost::exception_detail::clone_impl<boost::exception_detail::current_exception_std_exception_wrapper<std::bad_alloc> > std::exception::what: std::bad_alloc St9bad_alloc

4: ERROR: boost::exception: Throw location unknown (consider using BOOST_THROW_EXCEPTION) Dynamic exception type: boost::exception_detail::clone_impl<boost::exception_detail::current_exception_std_exception_wrapper<std::bad_alloc> > std::exception::what: std::bad_alloc St9bad_alloc

As a consequence, the output is not generated. Can anyone help me to solve this errors?

Thank you in advance!

RNA-Seq illumina fastq bcl2fastq • 9.2k views
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All of them sound like memory allocation errors and appear to be related to BOOST libraries (of which a specific version is needed for blc2fastq, if memory serves me right).

Is this a new install of bcl2fastq? Has it been validated/used for other data analysis?

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No, unfortunately it is not a new install and people used it to run their analysis. I totally don't know how to deal with this errors.

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Is this the only error? Have you looked through the entire log to see what else is there?
Is it possible that the admins updated BOOST libraries since? What OS is this on? Can you find out what version of BOOST is default?

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Yes, these are the only errors that appear. I don't know what boost version is. Do you think it is something I cannot solve by myself but only through the cluster admin?

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It would be best to contact the cluster admins and let them know that this is happening.

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Ok, thank you very much for your suggestions.

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8.7 years ago

Check the sample names in the sample sheet. They can't have ? ( ) [ ] / \ = + < > : ; " ' , * ^ | & . or spaces.

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Do you think this might be the problem? I will check the file.

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