10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
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bamtofastqerror: Not a valid read pair: false, false #103

Open MingwuDuan opened 2 years ago

MingwuDuan commented 2 years ago

Hi all, I downloaded the original bam file from SRA database and ran bamtofastq with "--traceback" twice, each time getting this error:

bamtofastqerror: Not a valid read pair: false, false
Please contact patrick@10xgenomics.com for assistance. Please re-run with --traceback and include stack trace with an error report
see below for more details:
==========================
Not a valid read pair: false, false
   0: failure::backtrace::internal::InternalBacktrace::new
             at execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/src/backtrace/internal.rs:46
      failure::backtrace::Backtrace::new
             at execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/src/backtrace/mod.rs:121
   1: <failure::error::error_impl::ErrorImpl as core::convert::From<F>>::from
             at execroot/exec/external/bamtofastq/execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/src/error/error_impl.rs:19
      <failure::error::Error as core::convert::From<F>>::from
             at execroot/exec/external/bamtofastq/execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/src/error/mod.rs:36
      failure::error_message::err_msg
             at execroot/exec/external/bamtofastq/execroot/home/registry/src/github.com-1ecc6299db9ec823/failure-0.1.8/src/error_message.rs:12
      bamtofastq::FormatBamRecords::bam_rec_to_ser
             at execroot/exec/external/bamtofastq/src/main.rs:494
   2: bamtofastq::proc_double_ended
             at execroot/exec/external/bamtofastq/src/main.rs:1185
      bamtofastq::inner
             at execroot/exec/external/bamtofastq/src/main.rs:1110
   3: bamtofastq::go
             at execroot/exec/external/bamtofastq/src/main.rs:1020
      bamtofastq::main
             at execroot/exec/external/bamtofastq/src/main.rs:977
   4: core::ops::function::FnOnce::call_once
             at /mnt/build/toolchains/tools/rust/1.53.0/lib/rustlib/src/rust/library/core/src/ops/function.rs:227
      std::sys_common::backtrace::__rust_begin_short_backtrace
             at /mnt/build/toolchains/tools/rust/1.53.0/lib/rustlib/src/rust/library/std/src/sys_common/backtrace.rs:125
   5: main
   6: __libc_start_main
   7: <unknown>

What should I do next ?