A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
The output log file does not have enough characters to report all information. The end is cu off if there are many runs, which prevents you from seeing how many times were retried:
executor > local (3331), slurm (140)
[- ] process > GEMmaker:get_software_versions -
[37/07bf7d] process > GEMmaker:retrieve_sra_metadata [100%] 1 of 1, cached: 1 ✔
[7c/6f31d1] process > GEMmaker:download_runs (SRX... [100%] 3422 of 3422, cac...
[3f/b578f2] process > GEMmaker:fastq_dump (SRX103... [100%] 3349 of 3349, cac...
[98/12cf92] process > GEMmaker:fastq_merge (SRX10... [ 99%] 3327 of 3349, cac...
[39/1f9b0a] process > GEMmaker:fastqc_1 (SRX13487... [ 99%] 3315 of 3332, cac...
[c8/786335] process > GEMmaker:kallisto (SRX10307... [ 99%] 3312 of 3327, cac...
[f5/8cba62] process > GEMmaker:kallisto_tpm (SRX1... [100%] 3312 of 3312, cac...
[85/49bc64] process > GEMmaker:next_sample (SRX84... [ 96%] 3263 of 3384
[- ] process > GEMmaker:multiqc -
[- ] process > GEMmaker:create_gem -
[- ] process > GEMmaker:failed_run_report -
[57/dc5ba0] process > GEMmaker:clean_work_files (... [ 99%] 9985 of 9986, cac...
[24/7f085f] process > GEMmaker:clean_work_dirs (S... [100%] 3312 of 3312, cac...
On a separate note, the output file is very annoying to look at, as much of the information is needlessly copied. This should be cleaned up so it is a more logical format.
Description of the bug
The output log file does not have enough characters to report all information. The end is cu off if there are many runs, which prevents you from seeing how many times were retried:
On a separate note, the output file is very annoying to look at, as much of the information is needlessly copied. This should be cleaned up so it is a more logical format.
Command used and terminal output
No response
Relevant files
No response
System information
No response