gzip: stdin: unexpected end of file \ zcat | split -l 1000000 - out. &&

[zhipengliux]

commond: tallynn nanopore make full -v5 --local
logfile:
pipeline.log

It seems that the fastq file is not read。

Looking forward to your reply!!

[Acribbs]

Looks like you dont have the fastq file in the correct directory, I believe that the pipeline defaults to requireing the inpiut fastq in a dir called "data.dir"

[zhipengliux]

Thanks for your reply!
This is my yml file.
pipeline.yml.txt

But occur annother error:
ValueError: --set-cell-barcode option specifies more cell barcodes than the number of observed cell barcodes. This may be because --subset-reads was set to a value too low to capture reads from all cells. 6 cell barcodes observed from 100000000 parsed reads. Expected>= 3000 cell barcodes \

How to set "--set-cell-barcode" ?
Looking forward to your reply!!

[Acribbs]

You have set the barcode using the whitelist: 3000. This is passed to the forked version of UMI-tools (https://github.com/Acribbs/UMI-tools and the branch AC-dualoligo), which will handle homodimer UMIs. This suggests that you dont have enough cells greater than 3000 within your dataset