Entering edit mode
10 months ago
tien
▴
10
Hello, I am trying to use cellranger for aligning data. I have two different datasets. I could successfully run cellranger count on the first one. However, the second dataset prompted error as following
[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']]
I tried to apply cellranger on only these two files and the same error was returned.
According to 10x , I ran md5sum -c on these two files, it returned OK for both. So I assumed that they were complete by using file checksums.
Is there any other reason or check that I should do? Or If anyone know how can I solve this problem?
Thanks in advance.
It may be best to validate if the files are not corrupt directly.
You can use a fastq validation program (https://github.com/nunofonseca/fastq_utils use
fastq_info) to check.Thanks a lot. I will try it.