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XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://xpresspipe.readthedocs.io/en/latest/
GNU General Public License v3.0
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Cannot alignment #54

Closed hailong-hu closed 2 months ago

hailong-hu commented 1 year ago

Describe the bug I successfully generated the reference according to "xpresspipe curateReference -o /path/to/reference -f /path/to/reference/genome_fastas -g /path/to/reference/transcripts.gtf"

Then I process the dataset according to "xpresspipe riboseq -i /path/to/input -o /path/to/output -r /path/to/reference/ --gtf /path/to/reference//transcripts_CT.gtf -e ribo"

The "triming", "QC" can be completed, but the alignment can not.

Error as shown as: "ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False"

Desktop (please complete the following information):

j-berg commented 1 year ago

Hi, Sorry for the delay. Could you provide me a sample FASTQ file, along with any log files you receive? You can email them to me at jordanberg.contact@gmail.com

Thanks!