hsun3163
hsun3163
Hi Frederik, thank you for pointing this out. We are working on the splicing events and encountered the same issue as well. I wonder do you have a good idea...
These two command fails: sos run pipeline/reference_data.ipynb download_hg_reference --cwd ../input/reference_data sos run pipeline/reference_data.ipynb download_dbsnp --cwd ../input/reference_data
could be firewall blocking ftps.
The download_dbsnp should be due to different firewall setting in different nodes. The download_hg_reference is more strange as it can be wget but not download() via sos. ``` ERROR: download_hg_reference...
It is unclear what makes the difference despite the success. It could be that the SINGULARITY_BIND variable in the csg was not properly recognized, but it contradicts the previous success.
> ``` > /opt/conda/bin/python: can't open file '/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/scripts/tmpdbgt_wz5/singularity_run_83472.py': [Errno 2] No such file or directory > ``` This is not a error by itself per se. SOS will move the...
As it occurs, the bam file is empty. Can you point me to the analysis notebook that documenting all your analysis as we discussed? ``` hs3163@csglogin:/mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test$ ls -lah /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961* -rw-r--r--...
please do document the analysis in the notebook going forward...it would be hard to keep track of bash scripts. that being said, how is ``` /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/xqtl_protocol_data_bam_list ``` generated ? This...
> for the star output step: I ran it multiple times (including test running with a smaller sample size ) - most of the time it ended with no error...
> Here is the summarized notebook of scripts and log files `/home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_contigs_GTF.ipynb` can you fork the fungi-QTL-analysis repo, and send a pr to upload this notebook (preferable along with other...