returned non-zero exit status 1

[francisfa]

Hi, There are some errors about that returned non-zero exit status1. I think this is a problem in python. But i do not how to fix it? I do not think I could change the python script. Any advices is OK. Thank you!

2018-10-11 21:06:25 [runtime] (update)          ID.normal2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0 chunks_running
2018-10-11 21:12:26 [runtime] (update)          ID.normal2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0 chunks_running
2018-10-11 21:15:08 [runtime] (failed)          ID.normal2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS

[error] Pipestance failed. Error log at:
normal2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u55bdbf4968/_errors

Log message:
Traceback (most recent call last):
  File "/test/software/cellranger-2.1.1/martian-cs/2.3.2/adapters/python/martian_shell.py", line 529, in _main
    stage.main()
  File "/test/software/cellranger-2.1.1/martian-cs/2.3.2/adapters/python/martian_shell.py", line 495, in main
    self._run(lambda: self._module.main(args, outs))
  File "/test/software/cellranger-2.1.1/martian-cs/2.3.2/adapters/python/martian_shell.py", line 464, in _run
    cmd()
  File "/test/software/cellranger-2.1.1/martian-cs/2.3.2/adapters/python/martian_shell.py", line 495, in <lambda>
    self._run(lambda: self._module.main(args, outs))
  File "/test/software/cellranger-2.1.1/cellranger-cs/2.1.1/mro/stages/common/chunk_reads/__init__.py", line 53, in main
    tk_subproc.check_call(chunk_reads_args)
  File "/test/software/cellranger-2.1.1/cellranger-cs/2.1.1/tenkit/lib/python/tenkit/log_subprocess.py", line 37, in check_call
    return subprocess.check_call(*args, **kwargs)
  File "/test/software/cellranger-2.1.1/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c9/lib/python2.7/subprocess.py", line 186, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', '/test/XX/RNAseq/Batch2_normal/normal2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u55bdbf4968/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status 1

[ikohideonbush]

@francisfa Could you tell me how this problem was resolved at last? I've just encountered the same situation and suspect the problem lies in my data. Thanks very much!

[francisfa]

@ikohideonbush Sorry for the delay. You should check the completeness of your data by using md5sum. Hope this helps.

[ikohideonbush]

@ikohideonbush Sorry for the delay. You should check the completeness of your data by using md5sum. Hope this helps. I realized it indeed was the fastq files' problem. Thanks!

[Yale73]

@francisfa @ikohideonbush I've just encountered the same situation. As I am a novice and I have no idea where the problem lies in. I tried to run the md5sum.,it failed. Could you tell me how to solve this problem? Many thanks.

[ikohideonbush]

@francisfa @ikohideonbush I've just encountered the same situation. As I am a novice and I have no idea where the problem lies in. I tried to run the md5sum.,it failed. Could you tell me how to solve this problem? Many thanks.

Hi friend， I am not very sure what your question is. Do you mean that you opened a shell, entered the data directory and run “md5sum -c <*the-md5file-you-were-given.txt>” and finally get error message?

[Yale73]

@ikohideonbush Thanks for your reply, I didn't run the right code. But I fixed the issue finally. I guess my problem is the ystem. My desktop linux is 32GB ram, 4 cores×8 logical processor. I ran the same code on our university cluster, it works. Thanks again!

[chris-rands]

I encountered a similar error with failure at the chunk_reads stage. While I found this failure is documented on the CR website: https://kb.10xgenomics.com/hc/en-us/articles/360004348051-Why-did-cellranger-count-fail-in-the-CHUNK-READS-stage-

It did not solve my issue. In my case the _stdout log is error free but _stderr contains:

[stderr]
thread 'main' panicked at 'index out of bounds: the len is 10 but the index is 10', libcore/slice/mod.rs:2046:10
[stderr]
thread 'main' panicked at 'index out of bounds: the len is 10 but the index is 10', libcore/slice/mod.rs:2046:10
note: Run with `RUST_BACKTRACE=1` for a backtrace.

Can anyone help? Thanks!

[evolvedmicrobe]

can you run it again after setting export RUST_BACKTRACE=1 and post the stack trace?

Also, feel free to directly contact support at support@10xgenomics.com for help debugging or fixing any issues.

[chris-rands]

@evolvedmicrobe thanks, here's the full traceback for another run:

[stderr]
thread 'main' panicked at 'index out of bounds: the len is 7 but the index is 7', libcore/slice/mod.rs:2046:10
stack backtrace:
   0: std::sys::unix::backtrace::tracing::imp::unwind_backtrace
             at libstd/sys/unix/backtrace/tracing/gcc_s.rs:49
   1: std::sys_common::backtrace::print
             at libstd/sys_common/backtrace.rs:71
             at libstd/sys_common/backtrace.rs:59
   2: std::panicking::default_hook::{{closure}}
             at libstd/panicking.rs:211
   3: std::panicking::default_hook
             at libstd/panicking.rs:227
   4: std::panicking::rust_panic_with_hook
             at libstd/panicking.rs:477
   5: std::panicking::continue_panic_fmt
             at libstd/panicking.rs:391
   6: rust_begin_unwind
             at libstd/panicking.rs:326
   7: core::panicking::panic_fmt
             at libcore/panicking.rs:77
   8: core::panicking::panic_bounds_check
             at libcore/panicking.rs:59
   9: chunk_reads::main
             at libcore/slice/mod.rs:2046
             at libcore/slice/mod.rs:1914
             at liballoc/vec.rs:1725
             at chunk_reads/src/main.rs:201
             at chunk_reads/src/main.rs:123
             at chunk_reads/src/main.rs:106
  10: std::rt::lang_start::{{closure}}
             at libstd/rt.rs:74
  11: std::panicking::try::do_call
             at libstd/rt.rs:59
             at libstd/panicking.rs:310
  12: __rust_maybe_catch_panic
             at libpanic_unwind/lib.rs:103
  13: std::rt::lang_start_internal
             at libstd/panicking.rs:289
             at libstd/panic.rs:392
             at libstd/rt.rs:58
  14: main
  15: __libc_start_main
  16: <unknown>
             at ../sysdeps/x86_64/elf/start.S:103

[chris-rands]

Update: in my case the error occurred because of trimming I applied to R2 reads to remove adapters. Not doing the trimming (the trimming is not recommended by 10X anyway) leads to no error

[evolvedmicrobe]

Thanks @chris-rands, glad this issue was solved. This code will be updated in future versions and will likely have a different error message.

[bazok100]

I am having similar issue and I am still not able to resolve

[danieletavernari]

In case someone still encountered this problem, a reason can be a corrupted/incomplete download of the FASTQ files. I solved by re-downloading the files.

[ThuyTien1]

Hello, I am having similar problem. stdout return

[stdout]
chunk_reads vVERSION
chunks: [("R1", "/test/Batch1_S1_L006_R1_001.fastq.gz", false), ("R2", "/test/Batch1_S1_L006_R2_001.fastq.gz", false)]
opening: "/test/Batch1_S1_L006_R1_001.fastq.gz"
opening: "/test/Batch1_S1_L006_R2_001.fastq.gz"
got recs: 28810048
got recs: 48304343
error: corrupt gzip stream does not have a matching checksum
caused by: corrupt gzip stream does not have a matching checksum
------------
If you believe this is a bug in chunk_reads, please report a bug to support@10xgenomics.com.

running chunk reads: [['chunk_reads', '--reads-per-fastq', '5000000', '/test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u90ff8a153e/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']]

However, when I ran md5sum -c on these two files, it returned OK for both. Is there any other reason or check that I should do? Or If anyone know how can I solve this problem?

Thanks in advance.