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cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
https://cumc.github.io/xqtl-protocol/
MIT License
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PSI quantification for alternative splicing events via Psichomics fails #440

Open jackytao18 opened 2 years ago

jackytao18 commented 2 years ago

The codes below are quoted from the notebook.

sos run splicing_calling.ipynb psichomics \
    --cwd psichomics_output/ \
    --samples sample_fastq_bam_list\
    --splicing_annotation hg38_suppa.rds \
    --container containers/psichomics.sif

One problem is that psichomics could not find where the splicing_annotation is using a relative path. This can be solved by inputting the full path of the suppa.eds file. However, it still doesn't work. My error messages and stderr are listed below.

errormessage stderr

Please help me fix it.

hsun3163 commented 2 years ago

The key msg here is 

Warning message:
In loadLocalFiles("/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/output/psichomics") :
  No supported files were found in the given folder.

indeed, the only file in the designated folder have only a x in it. 

hs3163@node92:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/output/psichomics$ ls
psi_raw_data.stderr  psi_raw_data.stdout  psichomics_junctions.txt
hs3163@node92:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/output/psichomics$
hs3163@node92:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/output/psichomics$
hs3163@node92:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing/output/psichomics$ cat psichomics_junctions.txt
x

@Rhopala are u familiar with this behavior?