Chunmingl

The bam files were intact, and the qc files looked ok. however, many more samples returned the same errors after rerunning from rnaseq call. @hsun3163 tail /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/output/rnaseq/test/PA00000961.rnaseqc.gene_tpm.gct.stderr ``` BAM file...

I submitted in bash scripts. Here are the some of the scripts I have previously run. ``` /home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_rnaseq3.sh /home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_rnaseq4.sh ```

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 message...

Here is the summarized notebook of scripts and log files `/home/cl4215/githubrepo/mrmash_ROSMAP/Knight/knight_contigs_GTF.ipynb`

Pr is sent

I received an error message /mnt/vast/hpc/csg/cl4215/ROSMAP/knight/errout/knight_staroutput7.log ``` ERROR: [picard_qc (picard_qc)]: [picard_qc]: Failed to execute process "bash(fr"""set -e\ntouch {_output[0]:n}.CollectMultipleMetrics...["cord_bam"].zap()\n\n" name 'job_size' is not defined [STAR_output]: Exits with 1 pending step (STAR_output)...