pigeon make-seurat error: could not open plain text file

[JiangyanYu]

I am using smrttools v13. At the last step of pigeon make-seurat, I receive this error:

pigeon make-seurat --dedup /home/852-2/corrected/852-2.dedup.fasta --group /home/852-2/mapped/852-2.collapsed.group.txt -d /home/852-2/seurat /home/852-2/mapped/852-2_classification.filtered_lite_classification.txt --log-level DEBUG --log-file /home/852-2/seurat/log.txt

20240205 11:19:44.058 | FATAL | pigeon make-seurat ERROR: [pbbam] text file writer ERROR: could not open plain text file: file: /home/852-2/seurat//home/852-2/mapped/852-2.annotated.info.csv reason: No such file or directory

It seems that the xxx.annotated.info.csv file is in the same location as the xxx.classification.filtered_lite_classification.txt. Therefore I copy the xx.classification.filtered_lite_classification.txt to current working directory. This solved the problem:

pigeon make-seurat --dedup /home/852-2/corrected/852-2.dedup.fasta --group /home/852-2/mapped/852-2.collapsed.group.txt -d /home/852-2/seurat 852-2_classification.filtered_lite_classification.txt --log-level DEBUG --log-file /home/852-2/seurat/log.txt

Is this the correct way to bypass the error? Or is this a bug in this version? Thanks!

[armintoepfer]

Please reach out to support@pacb.com, thank you!

[omarelgarwany]

I solved this issue by using the --output-prefix flag:

-o,--out-prefix STR Prefix for all, non-matrix files. If not specified, the primary input classification file will be used to determine the prefix. Example: 'my_isoforms_classification.filtered_lite_classification.txt' or 'my_isoforms_classification.txt' input will yield output prefix 'my_isoforms'.