<p>I'm using Cellranger for alignment on scRNA-seq data but got the following error message:</p>
<pre><code>CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', '/path/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u1b14459fe6/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status 101
</code></pre>
<p>I performed <code>md5sum</code> on all fastq files and received OK.
May I ask what can be reason for this error and how can I detect it and fix it?</p>
<p>Thanks for any help.</p>

CC BY-SA 4.0
2024-05-17T11:03:52.603Z
"I performed md5sum on all fastq files and received OK" Could you explain this please? OK in this context only make sense if you are comparing the hashes to a previous run, it doesn't tell us anything about the files other than that they are identical to some other files. What exactly did you compare to? What are your input files? Are they compressed? How? If with gzip, what does `gzip -t YOUR_FILE && echo OK || echo BAD` return?
terdon
CC BY-SA 4.0
2024-05-18T19:57:45.253Z
This is not a full error message; it is an indication that there was an error. Does the program provide any additional information beyond this message you have seen?
gringer
<cellranger>
Cellranger count failed at detect chemistry
# Cellranger count failed at detect chemistry

(Asked by: username_0 on 2024-05-17)

I'm using Cellranger for alignment on scRNA-seq data but got the following error message:
CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', '/path/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u1b14459fe6/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status 101

I performed md5sum on all fastq files and received OK.
May I ask what can be reason for this error and how can I detect it and fix it?
Thanks for any help.

**Tags:** cellranger
> **Comments:**
> **username_1**: "I performed md5sum on all fastq files and received OK" Could you explain this please? OK in this context only make sense if you are comparing the hashes to a previous run, it doesn't tell us anything about the files other than that they are identical to some other files. What exactly did you compare to? What are your input files? Are they compressed? How? If with gzip, what does `gzip -t YOUR_FILE && echo OK || echo BAD` return?  
> **username_2**: This is not a full error message; it is an indication that there was an error. Does the program provide any additional information beyond this message you have seen?  

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## 0 answers

