[error] No input FASTQs were found with the requested sample indices.

Question: When I was running my gene expression sample with the feature barcoding data, I got this error [error] No input FASTQs were found with the requested sample indices. What does this mean?

Answer: At a high level, this means that the FASTQ/sample combination given on the command line, or in the library CSV file, doesn't match the actual FASTQ files. There could be several causes of this error. Here are a few common causes with ways you might correct them:

1. Specified the wrong path to the FASTQ files. Please specify the path all the way to the directory containing the correct FASTQ files. Also note that extra directories and file can affect FASTQ parsing, so removing non-FASTQ files from the FASTQ directory may also resolve issues.
2. Specified wrong sample names. The sample column is the same as the --sample argument to cellranger count, which should be the prefix of the FASTQ file name (string before _S). There is more about FASTQ naming requirements in this article. 
3. Hidden characters in the Libraries CSV File. This article addresses a similar issue.

For more information on about correct Libraries CSV File format please see our Feature barcoding analysis page. And for more information about specifying input FASTQ please see our Specifying Input FASTQ Files page.

If you need further assistance, feel free to contact us at support@10xgenomics.com.