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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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segmentation fault #2633

Closed DiyaVaka closed 5 years ago

DiyaVaka commented 5 years ago

terminate called after throwing an instance of 'libmaus2::exception::LibMausException' what(): PosixOutputStreamBuffer::doSync(): write() failed: No space left on device /mnt/bcbio/anaconda/share/biobambam-2.0.87-1/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x4c)[0x7f28d4ab1f8c] bamsormadup(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x41fc10] bamsormadup(libmaus2::aio::PosixFdOutputStreamBuffer::doWrite(int, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, char, unsigned long, long, unsigned long)+0x255)[0x427e35] bamsormadup(libmaus2::aio::PosixFdOutputStreamBuffer::doSync()+0x51)[0x427f31] bamsormadup(libmaus2::aio::PosixFdOutputStreamBuffer::sync()+0x12)[0x428172] /mnt/bcbio/anaconda/share/biobambam-2.0.87-1/bin/../lib/libstdc++.so.6(std::ostream::flush()+0x1e)[0x7f28d3f054be] /mnt/bcbio/anaconda/share/biobambam-2.0.87-1/bin/../lib/libmaus2.so.2(std::_Sp_counted_ptr<libmaus2::aio::PosixFdOutputStream, (__gnu_cxx::_Lock_policy)2>::_M_dispose()+0x57)[0x7f28d4a95cc7] bamsormadup()[0x41790a] bamsormadup()[0x418548] bamsormadup()[0x46e818] bamsormadup()[0x46e892] bamsormadup()[0x41790a] bamsormadup()[0x49ecc8] bamsormadup()[0x4bfa1e] bamsormadup()[0x4c0499] bamsormadup()[0x514ec8] bamsormadup()[0x41afce] bamsormadup()[0x41524f] /lib64/libc.so.6(libc_start_main+0xf5)[0x7f28d1473445] bamsormadup()[0x416f22] /bin/bash: line 1: 6461 Segmentation fault bamcat level=0 tmpfile=/mnt/bcbiotx/tmpWV7hU3/bcbiotx/tmpG6BaBr/NG14-sort.bam-bammerge cat /mnt/bcbiotx/tmpWV7hU3/bcbiotx/tmpG6BaBr/NG14-sort.list 6462 Aborted | bamsormadup threads=16 tmpfile=/mnt/bcbiotx/tmpWV7hU3/bcbiotx/tmpG6BaBr/NG14-sort.bam-bamsormaduptmp indexfilename=/mnt/bcbiotx/tmpWV7hU3/bcbiotx/tmpG6BaBr/NG14-sort.bam.bai > /mnt/bcbiotx/tmpWV7hU3/bcbiotx/tmpG6BaBr/NG14-sort.bam ' returned non-zero exit status 134

roryk commented 5 years ago

Hi @DiyaVaka, are you running out of space in /mnt/bcbiotx? The key error here is terminate called after throwing an instance of 'libmaus2::exception::LibMausException' what(): PosixOutputStreamBuffer::doSync(): write() failed: No space left on device

roryk commented 5 years ago

Closing as this seems like a specific issue which is outside of bcbio.