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