Error during LDrefinement

[Thapeachydude]

Hi,

I'm encountering an error during the final step of the SNV calling tutorial for scRNA-Seq data.
Specifically, I get:

[2024-05-21 17:09:53,243] INFO     Monopogen.py Run LD refinement ...
Rscript /cluster/work/moor/marcel_prj/Monopogen/apps/../src/LDrefinement.R  /cluster/work/moor/loop_prj_analysis/monopogen/bam/somatic/chr11.gl.filter.hc.cell.mat.gz /cluster/work/moor/loop_prj_analysis/monopogen/bam/somatic/ chr11
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
  incorrect number of dimensions
Calls: SVM_train
Execution halted
[2024-05-21 17:10:23,988] ERROR    Monopogen.py In LDrefinement step chr11 failed!
[2024-05-21 17:10:23,989] ERROR    Monopogen.py Failed! See instructions above.

Any insights into what is causing this would be much appreciated.

Many thanks and best regards : )

[ValerieMarot]

Hi,

I'm encountering a very similar error during the last step on my own data:

[2024-05-22 09:35:55,483] INFO     Monopogen.py Run LD refinement ...
Rscript apps/../src/LDrefinement.R  run_data/A10//somatic/chr21.gl.filter.hc.cell.mat.gz run_data/A10//somatic/ chr21
Error in test_x[, colnames(test_x) == "QS"] : 
  incorrect number of dimensions
Calls: SVM_train
Execution halted
[2024-05-22 09:35:57,114] ERROR    Monopogen.py In LDrefinement step chr21 failed!
[2024-05-22 09:35:57,114] ERROR    Monopogen.py Failed! See instructions above.

Any help would also be very much appreciated! And thank you for developing and maintaining such a nice method :)

[jinzhuangdou]

Hi, could you please share the file named chr*.gl.vcf.filter.DP4 with me for troubleshooting purposes? Thank you!

[Thapeachydude]

Hi,

the first few lines look like this:

chr11   207185  G       A       1       0.0     0.0     1.0     0.0     NA      None    0.0     None    None    None    None    -0.38   0.0
chr11   208001  C       T       1       0.0     0.0     0.0     1.0     NA      None    0.0     None    None    None    None    -0.38   0.0
chr11   288042  C       A       1       0.0     0.0     0.0     1.0     NA      None    0.0     None    None    None    None    -0.38   0.0
chr11   288115  T       C       1       0.0     0.0     0.0     1.0     0|1     None    0.0     None    None    None    None    -0.38   0.0
chr11   308290  T       C       2       0.0     0.0     0.0     2.0     1|0     0.1     0.0     None    None    None    None    -0.45   0.0

Would you have an e-mail address I can send the full file to?

[jinzhuangdou]

Could you try the updated version. I have just fixed this issue yesterday since some features used for SVM trainning are not available in your files. Let me know if you still have problems. Thanks

[Thapeachydude]

I pulled the latest version and re-ran everything.
LDrefinement still fails. chr*.gl.vcf.filter.DP4 now looks like this.

chr11	207185	G	A	1	0.0	0.0	1.0	0.0	NA	None	0.0	None	None	None	None	-0.38	0.0
chr11	208001	C	T	1	0.0	0.0	0.0	1.0	NA	None	0.0	None	None	None	None	-0.38	0.0
chr11	288042	C	A	1	0.0	0.0	0.0	1.0	NA	None	0.0	None	None	None	None	-0.38	0.0
chr11	288115	T	C	1	0.0	0.0	0.0	1.0	1|0	None	0.0	None	None	None	None	-0.38	0.0
chr11	308290	T	C	2	0.0	0.0	0.0	2.0	0|1	0.1	0.0	None	None	None	None	-0.45	0.0
chr11	308363	G	C	2	0.0	1.0	0.0	1.0	0|1	None	0.5	1.0	1.0	1.0	None	-0.38	0.0
chr11	309069	C	T	4	0.0	3.0	0.0	1.0	NA	None	0.75	1.0	1.0	1.0	None	-0.38	0.0
chr11	309127	A	G	3	0.0	1.0	0.0	2.0	0|1	0.8	0.33	1.0	1.0	1.0	None	-0.45	0.0
chr11	314969	T	G	5	0.0	4.0	0.0	1.0	NA	None	0.8	1.0	1.0	1.0	None	-0.38	0.0
chr11	320649	G	A	4	1.0	0.0	3.0	0.0	NA	0.02	0.25	1.0	1.0	1.0	None	-0.51	0.0

[jinzhuangdou]

Is it possible that you can share one chr*.gl.vcf.filter.DP4 with me so that I can give a trouble shooting? Thanks

[Thapeachydude]

Hi, you can get the file for chr11 here.

[aidanshoham12]

Hello, Ive been having the same issue in the LD refinement module, here is the error message message im getting:
python ${path}/src/Monopogen.py somatic -a ${path}/apps -r ${path}/lab_samples/region_lst/region.lst -t 1 -i ${path}/lab_samples/outputs/sample_name -l ${path}/lab_samples/csv_files/csv_somatic.csv -s LDrefinement -g ${path}/example/hg38.fa [2024-06-13 16:08:42,935] INFO Monopogen.py Run LD refinement ... Rscript /path/to/src/LDrefinement.R /path/to/somatic/chr20.gl.filter.hc.cell.mat.gz /path/to/somatic/ chr20 sh: Rscript: command not found [2024-06-13 16:08:43,051] ERROR Monopogen.py In LDrefinement step chr20 failed! [2024-06-13 16:08:43,051] ERROR Monopogen.py Failed! See instructions above.
For reference I pulled the code from GitHub on June 6. For reference, here is what happens when I head chr*.gl.vcf.filter.DP4.
chr20 251727 C G 123 0.0 0.0 0.0 4.0 1|0 0.63 0.0 None None None None -0.56 0.0
chr20 258018 C T 77 0.0 0.0 5.0 70.0 1|1 0.07 0.0 None None None 1.0 -0.69 0.0
Let me know if you have any suggestions to get it to work.
Thank you so much!

[Vann6]

I encountered an same issue with LDrefinement.R. In LDrefinement.R, when running mutation_block <- SNV_block(summary=meta) and svm_in <- SVM_prepare(mutation_block), either svm_in$test or svm_in$train is empty. Consequently, svm_out <- SVM_train(label = svm_in, dir = outdir, region = region) throws an error: Error in test_x[, colnames(test_x) == "QS"] : incorrect number of dimensions. I've verified that the input files are correct. Can you refine SUM-train and LDrefinement.R to handle svm_in$test or svm_in$train is empty. Below are my tested files. Thank you!
chr4.gl.filter.hc.cell.mat.gz
chr3.gl.filter.hc.cell.mat.gz

[WaqarHusain]

Hi, I am facing the same issue. Below is my log from LDRefinement.

[2024-08-26 11:45:29,866] INFO Monopogen.py Run LD refinement ...
[1] 108
[1] 108
[1] "/mypath/somatic/chr1.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 69
[1] 69
[1] "/mypath/somatic/chr11.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 37
[1] 37
[1] "/mypath/somatic/chr16.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 27
[1] 27
[1] "/mypath/somatic/chr22.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 24
[1] 24
[1] "/mypath/somatic/chr14.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 51
[1] 51
[1] "/mypath/somatic/chr2.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 46
[1] 46
[1] "/mypath/somatic/chr12.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 46
[1] 46
[1] "/mypath/somatic/chr6.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 64
[1] 64
[1] "/mypath/somatic/chr8.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 50
[1] 50
[1] "/mypath/somatic/chr3.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 37
[1] 37
[1] "/mypath/somatic/chr4.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 21
[1] 21
[1] "/mypath/somatic/chr20.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 47
[1] 47
[1] "/mypath/somatic/chr7.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 56
[1] 56
[1] "/mypath/somatic/chr17.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 61
[1] 61
[1] "/mypath/somatic/chr19.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 35
[1] 35
[1] "/mypath/somatic/chr9.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 27
[1] 27
[1] "/mypath/somatic/chr15.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 15
[1] 15
[1] "/mypath/somatic/chr21.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 25
[1] 25
[1] "/mypath/somatic/chr13.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 60
[1] 60
[1] "/mypath/somatic/chr5.cell_snv.cellID.filter.csv"
Error in train_x_neg[, colnames(train_x_neg) == "QS"] :
incorrect number of dimensions
Calls: SVM_train
Execution halted
[1] 13
[1] 13
[1] "/mypath/somatic/chr18.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[1] 52
[1] 52
[1] "/mypath/somatic/chr10.cell_snv.cellID.filter.csv"
Error in train_x_pos[, 1] <- vec : replacement has length zero
Calls: SVM_train
Execution halted
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr1 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr11 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr16 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr22 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr14 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr2 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr12 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr6 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr8 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr3 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr4 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr20 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr7 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr17 failed!
[2024-08-26 11:45:52,336] ERROR Monopogen.py In LDrefinement step chr19 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr9 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr15 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr21 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr13 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr5 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr18 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py In LDrefinement step chr10 failed!
[2024-08-26 11:45:52,337] ERROR Monopogen.py Failed! See instructions above.