Closed mpoelchau closed 3 years ago
Thank @monica for providing the detail about the error. I modified the subprocess of the "efilter" to exclude records that have PACBIO_SMRT in the Platform field. I also tested the download_sra_metadata.py with the command: "download_sra_metadata.py -t 27457 -o 27457.tsv " The modified download_sra_metadata.py is in the PACBIO branch #47
Thanks :D
This is merged. closing.
@ShangYuChiang recently ran into an issue where the pipeline couldn't handle data from PacBio RS II (specifically, this experiment: https://www.ncbi.nlm.nih.gov/sra/SRR6023533). I believe it fails here (https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/master/rnannot/RNAseq_annotate.py#L109) since the following step (normalization) can't find the file output.fastq; and the trimmomatic error log reports
Error: Unable to detect quality encoding
After discussing this, we'll want to do 2 things:
In order to do 1., we need to update
download_sra_metadata.py
to exclude records that havePACBIO_SMRT
in thePlatform
field (probably usingefilter
). @ShangYuChiang do you think you can try this?Error message for reference:
and