Error in import10xFeatureMatrix - rownames (genes) of individual RNA objects are not equivalent.

[sureshsatpati]

Hello Team,

I’m encountering an issue while running multiome analyses on 7 samples. Specifically, I’m receiving the following error during the process:
Command used:
seRNA_new <- import10xFeatureMatrix(input = c("Common_Cells/input/10-DD/filtered_feature_bc_matrix.h5","Common_Cells/input/10-WD/filtered_feature_bc_matrix.h5","Common_Cells/input/1-DD/filtered_feature_bc_matrix.h5","Common_Cells/input/1-WD/filtered_feature_bc_matrix.h5","Common_Cells/input/4-DD-A/filtered_feature_bc_matrix.h5","Common_Cells/input/4-DD-B/filtered_feature_bc_matrix.h5","Common_Cells/input/4-WD/filtered_feature_bc_matrix.h5"), names = c('10-DD','10-WD','1-DD','1-WD','4-DD-A','4-DD-B','4-WD'), strictMatch = TRUE)

Complete log:

Setting default genome to Hg38.
Using GeneAnnotation set by addArchRGenome(Hg38)!
Using GeneAnnotation set by addArchRGenome(Hg38)!
ArchR logging to : ArchRLogs/ArchR-createArrows-1ceb6d6eaaf77-Date-2025-02-07_Time-11-34-23.986552.log
If there is an issue, please report to github with logFile!
2025-02-07 11:34:24.078139 : Batch Execution w/ safelapply!, 0 mins elapsed.
2025-02-07 11:34:24.222219 : (1-DD : 1 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.002 mins elapsed.
2025-02-07 11:34:24.373024 : (4-DD-B : 2 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.005 mins elapsed.
2025-02-07 11:34:24.464346 : (4-DD-A : 3 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.006 mins elapsed.
2025-02-07 11:34:24.601854 : (10-WD : 4 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.009 mins elapsed.
2025-02-07 11:34:24.692857 : (10-DD : 5 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.01 mins elapsed.
2025-02-07 11:34:24.788658 : (1-WD : 6 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.012 mins elapsed.
2025-02-07 11:34:24.908244 : (4-WD : 7 of 7) Arrow Exists! Marking as completed since force = FALSE!, 0.014 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-createArrows-1ceb6d6eaaf77-Date-2025-02-07_Time-11-34-23.986552.log
Importing Feature Matrix 1 of 7
Importing Feature Matrix 2 of 7
Importing Feature Matrix 3 of 7
Importing Feature Matrix 4 of 7
Importing Feature Matrix 5 of 7
Importing Feature Matrix 6 of 7
Importing Feature Matrix 7 of 7
Re-ordering RNA matricies for consistency.
Merging individual RNA objects...

Merging 10-WD

Merging 1-DD
Error in import10xFeatureMatrix(input = c("Common_Cells/input/10-DD/filtered_feature_bc_matrix.h5", :
Error - rownames (genes) of individual RNA objects are not equivalent.

package.version('ArchR')
[1] "1.0.2"

Using R version 4.3.3

I attempted to follow the advice from our previous discussions, but I’m still unable to resolve the issue. Could you please assist in troubleshooting this error? I’ve included the log I used for reference.

Thanks in advance for your help!

[immanuelazn]

Hi @sureshsatpati , we recently updated ArchR with a plethora of changes. Could you tell me if you're still facing these issues with these changes?

[sureshsatpati]

Thanks for the update! I haven't had a chance to test the recent changes yet. I have been using these version. Do you have any new update?

Appreciate the follow-up!

Best,
Suresh

[sureshsatpati]

Hello Team,
I have the updated and latest installation but I see same issue while running multiome analyses on 7 samples. Please suggest me how to proceed with this.
Your efforts are highly appreciated!
Thanks,
Suresh