Closed yuyingxie closed 3 years ago
evolvedmicrobe
commented
3 years ago Please contact support@10xgenomics.com for help with this issue, at first glance it looks like a transient file system error, but they'll be able to help you track this down.
zgyaru
commented
1 year ago Hi Yuying, I have countered the same error. Did you fix it?
plijnzaad
commented
1 year ago Hi all,
I occasionally get very similar crashes. I suspect NFS may be part of the problem, perhaps in conjunction with very long filenames / pathnames. Would very much like to see this solved ...
On the off chance that this is relevant, the crashes tend to happen at night, and the disks are mounted from an Isilon storage system ( DELL/EMC PowerScale OneFS )
erlun1
commented
6 months ago I confirm that this issue is due to insufficient disk space allocated to cellranger.
Dear Cellranger,
I am running the following codes to process my fastq data
cellranger count --id=Sample8_GE \ --transcriptome=refdata-gex-mm10-2020-A \ --fastqs=Sample_2571-YL-22 \ --localcores=8 \ --localmem=64
and got the following error message
2021-03-15 11:41:47 [runtime] (failed) ID.Sample5_GE.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD
[error] Pipestance failed. Error log at: Sample5_GE/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u01d54f79de/_errors
Log message: stage failed unexpectedly: 'internal error: entered unreachable code' execroot/home/registry/src/github.com-1ecc6299db9ec823/shardio-0.7.3/src/lib.rs:411: 0: martian::martian_entry_point::{{closure}} at execroot/exec/lib/rust/execroot/home/git/checkouts/martian-rust-35615836cc90309f/8b43658/martian/src/lib.rs:184:25 1: std::panicking::rust_panic_with_hook at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/std/src/panicking.rs:597:17 2: std::panicking::begin_panic::{{closure}} at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/std/src/panicking.rs:522:9 3: std::sys_common::backtrace::__rust_end_short_backtrace at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/std/src/sys_common/backtrace.rs:141:18 4: std::panicking::begin_panic at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/std/src/panicking.rs:521:12 5: shardio::BufferStateMachine<T,H>::close at execroot/exec/lib/rust/execroot/home/registry/src/github.com-1ecc6299db9ec823/shardio-0.7.3/src/lib.rs:411:37 shardio::ShardWriterInner<T,S>::close at execroot/exec/lib/rust/execroot/home/registry/src/github.com-1ecc6299db9ec823/shardio-0.7.3/src/lib.rs:656:27 shardio::ShardWriter<T,S>::finish at execroot/exec/lib/rust/execroot/home/registry/src/github.com-1ecc6299db9ec823/shardio-0.7.3/src/lib.rs:249:30 6: <shardio::ShardWriter<T,S> as core::ops::drop::Drop>::drop at execroot/exec/lib/rust/execroot/home/registry/src/github.com-1ecc6299db9ec823/shardio-0.7.3/src/lib.rs:271:18 core::ptr::drop_in_place at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/core/src/ptr/mod.rs:175:1 core::ptr::drop_in_place at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/core/src/ptr/mod.rs:175:1 7: core::ptr::drop_in_place at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/core/src/ptr/mod.rs:175:1
::run_get_error at execroot/exec/lib/rust/execroot/home/git/checkouts/martian-rust-35615836cc90309f/8b43658/martian/src/lib.rs:131:9 martian::MartianAdapter::run at execroot/exec/lib/rust/execroot/home/git/checkouts/martian-rust-35615836cc90309f/8b43658/martian/src/lib.rs:124:9 cr_lib::main at execroot/exec/lib/rust/cr_lib/src/bin/cr_lib.rs:111:23 10: core::ops::function::FnOnce::call_once at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/core/src/ops/function.rs:227:5 std::sys_common::backtrace::__rust_begin_short_backtrace at /rustc/e1884a8e3c3e813aada8254edfa120e85bf5ffca/library/std/src/sys_common/backtrace.rs:125:18 11: main 12: __libc_start_main 13:
at /mnt/home/adam.azarchs/crosstool/build/src/glibc-2.12.2/csu/../sysdeps/x86_64/elf/start.S:103
Waiting 6 seconds for UI to do final refresh.
Pipestance failed. Use --noexit option to keep UI running after failure.
Can you help me to debug it?
Thanks so much for your help.
Yuying