count matrix outputted with all zeros

[rayajallad]

Hello,

I am trying to run the pipeline but the count matrix has all zeros for everything each time. Another issue is that I specify 'gene_id' for annotations but the matrix produced has gene names instead.

Some things I found in the countmatrix.out that might be the reason I get all zeros are these unfinished steps (note that there are plenty more of these unfinished steps):

count jobs 1 align_bowtie2 1^[[0m ^[[33m/share/apps/bowtie2/2.4.2/bowtie2 -p 15 -x /scratch/work/cgsb/genomes/Public/Invertebrate/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans.WBcel235.dna.toplevel -U /scratch/projects/fitchlab/rj1435/count$ [Mon Nov 7 11:24:08 2022] Finished job 21. 4 of 23 steps (17%) done [Mon Nov 7 11:31:56 2022] Finished job 17. 5 of 23 steps (22%) done [Mon Nov 7 11:34:58 2022] Finished job 18. 6 of 23 steps (26%) done [Mon Nov 7 11:39:13 2022] Finished job 16. 7 of 23 steps (30%) done [Mon Nov 7 11:53:53 2022] Finished job 19. 8 of 23 steps (35%) done [Mon Nov 7 11:54:09 2022] Finished job 20. 9 of 23 steps (39%) done

another one:

^[[33mtouch _done_combodemultiplex_sam^[[0m Dynamically updating jobs [Mon Nov 7 11:55:23 2022] Finished job 15. 10 of 589 steps (2%) done

I was hoping to get some help on why all my matrices continue to only have zeros in them.

Thanks! Raya