Question: How do I solve the error "ERROR: There were no reads to process."?
Answer: The error can arise for two possible reasons. A common source of error is typos in the FASTQ file names. Another source of error is R1 reads that are shorter than the minimum required read length, e.g. 25 bases when 26 is expected.
(1) Typos
Please double-check file names are consistent and follow the expected naming convention illustrated on https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input, i.e. adhere to the format {samplename}_S{#}_L{###}_R{#}_{###).fastq.gz as follows.
test_sample1_S1_L001_R1_001.fastq.gz
test_sample1_S1_L001_R2_001.fastq.gz
Again, be sure the sample name is identical across the FASTQ set's R1 and R2 files and I1 and I2 if present. If you require further assistance, please share a screenshot of the FASTQ directory with file sizes, e.g. with ls -ltrh {directory} to support@10xgenomics.com.
(2) Shorter than expected R1 read lengths
Different chemistries have different expected minimum R1 read lengths, as shown in the table below.
If you are unsure what your read lengths are, you can peek into each FASTQ with zcat your.fastq.gz | less or run FastQC on the reads.
Shorter R1 reads could increase UMI duplicates. Please see the bottom of https://kb.10xgenomics.com/hc/en-us/articles/360053937392 for discussion on implications. If you require further assistance, please contact support@10xgenomics.com.