Noncoding analysis results using STAARpipelineSummary

[1874309276]

您好，我利用下列信息进行结果整理时出现了结果报错，您遇到过这种情况吗，可以帮忙看一下吗？超级感谢！
Gene_Centric_Noncoding_Results_Summary(agds_dir=agds_dir,gene_centric_noncoding_jobs_num=gene_centric_noncoding_jobs_num,
input_path=input_path,output_path=output_path,gene_centric_results_name=gene_centric_results_name,
ncRNA_jobs_num=ncRNA_jobs_num,ncRNA_input_path=ncRNA_input_path,
ncRNA_output_path=ncRNA_output_path,ncRNA_results_name=ncRNA_results_name,
obj_nullmodel=obj_nullmodel,known_loci=known_loci,
method_cond=method_cond,
QC_label=QC_label,geno_missing_imputation=geno_missing_imputation,variant_type=variant_type,
Annotation_dir=Annotation_dir,Annotation_name_catalog=Annotation_name_catalog,
Use_annotation_weights=Use_annotation_weights,Annotation_name=Annotation_name,
alpha=alpha,manhattan_plot=TRUE,QQ_plot=TRUE)

报错：
Error in rbind(results_downstream_genome, results) :
number of columns of matrices must match (see arg 2)
Calls: Gene_Centric_Noncoding_Results_Summary -> rbind
Execution halted

[yuxinyuanqt]

Thanks for your message.

This error is triggered at the very beginning of the function
Gene_Centric_Noncoding_Results_Summary, specifically around line 152 of the source code:

### downstream
if (results[3] == "downstream") {
  results_downstream_genome <- rbind(results_downstream_genome, results)
}

The error

Error in rbind(results_downstream_genome, results) :
number of columns of matrices must match

indicates that the object results being appended does not have the same structure (number of columns) as results_downstream_genome. From this error message alone, it is not possible to determine the exact cause.

To debug this, could you please provide more detailed information, in particular:

• Please check one gene_centric_noncoding_job result file (before summarization).
• The returned object should be a list, where
  • each element corresponds to one gene, and
  • each gene contains results for 7 noncoding masks (e.g. upstream, downstream, UTR, promoter_CAGE, promoter_DHS, enhancer_CAGE, enhancer_DHS).
• The length of these 7 mask-specific results should be consistent across genes.
  • It is acceptable for a mask to be NULL (meaning no result for that mask),
  • but the overall structure (a list of 7 elements per gene) should be the same.

Could you please verify whether your result file has a structure similar to the screenshot I shared (i.e. a list where each gene has 7 noncoding mask entries with consistent lengths or NULL)?

[1874309276]

谢谢你的留言。

该错误在函数Gene_Centric_Noncoding_Results_Summary的开头触发，具体位置为源代码第152行：

### downstream
if (results[3] == "downstream") {
  results_downstream_genome <- rbind(results_downstream_genome, results)
}

错误

Error in rbind(results_downstream_genome, results) :
number of columns of matrices must match

表示被附加对象的结构（列数）与 不同。仅凭这个错误信息，无法确定确切原因。results ``results_downstream_genome

为了调试这个问题，能否提供更详细的信息，特别是：

• 请在摘要前查看一个gene_centric_noncoding_job结果文件。
• 返回对象应为列表，其中
  • 每个元素对应一个基因，
  • 每个基因包含7种非编码掩蔽的结果（例如上游、下游、UTR、promoter_CAGE、promoter_DHS、enhancer_CAGE、enhancer_DHS）。
• 这7个面罩特异性结果的长度应在不同基因间保持一致。
  • 遮罩为NULL（即该掩码没有结果）是可以接受的，
  • 但整体结构（每个基因包含7个元素）应保持相同。

请你确认一下你的结果文件是否有类似我分享的截图结构（比如每个基因有7个长度一致的非编码掩码条目或NULL）？

您好，我查看了其中一个结果文件，好像是没有问题的，下面是报错文件的全部内容，我在想是不是因为其中某个文件结果没有跑成功呢，我该如何排查这个文件呢？🤔
Command-line arguments:
$adgs_path
[1] "/public/home/wubs/AD_WGS/STAAR/STEP_0/agds_dir.Rdata"

$null_path
[1] "/public/home/ylzhao/WGS/ventricles/starr/full_25.5.12_structure/STEP_1/z_EI_rint/obj_nullmodel_z_EI_rint.Rdata"

$anno_path
[1] "/home1/wubs/AD_WGS/STAAR/STEP_0/Annotation_name_catalog.Rdata"

$known_path
NULL

$noncoding_dir
[1] "/public/home/ylzhao/WGS/ventricles/starr/full_25.5.12_structure/STEP_3.2/z_EI_rint/"

$noncoding_prefix
[1] "z_EI_rint_Noncoding"

$ncRNA_dir
[1] "/public/home/ylzhao/WGS/ventricles/starr/full_25.5.12_structure/STEP_3.2/z_EI_rint/"

$ncRNA_prefix
[1] "z_EI_rint_ncRNA"

$output_dir
[1] "/public/home/ylzhao/WGS/ventricles/starr/full_25.5.12_structure/result_summary/STEP_3.2/z_EI_rint/"

$alpha
[1] 3.57e-07

Warning: --cond not provided. known_loci set to NULL.
Number of noncoding input files: 387
Number of ncRNA input files: 223
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
[1] 21
[1] 22
[1] 23
[1] 24
[1] 25
[1] 26
[1] 27
[1] 28
[1] 29
[1] 30
[1] 31
[1] 32
[1] 33
[1] 34
[1] 35
[1] 36
[1] 37
[1] 38
[1] 39
[1] 40
[1] 41
[1] 42
[1] 43
[1] 44
[1] 45
[1] 46
[1] 47
[1] 48
[1] 49
[1] 50
[1] 51
[1] 52
[1] 53
[1] 54
[1] 55
[1] 56
[1] 57
[1] 58
[1] 59
[1] 60
[1] 61
[1] 62
[1] 63
[1] 64
[1] 65
[1] 66
[1] 67
[1] 68
[1] 69
[1] 70
[1] 71
[1] 72
[1] 73
[1] 74
[1] 75
[1] 76
[1] 77
[1] 78
[1] 79
[1] 80
[1] 81
[1] 82
[1] 83
[1] 84
[1] 85
[1] 86
[1] 87
[1] 88
[1] 89
[1] 90
[1] 91
[1] 92
[1] 93
[1] 94
[1] 95
[1] 96
[1] 97
[1] 98
[1] 99
[1] 100
[1] 101
[1] 102
[1] 103
[1] 104
[1] 105
[1] 106
[1] 107
[1] 108
[1] 109
[1] 110
[1] 111
[1] 112
[1] 113
[1] 114
[1] 115
[1] 116
[1] 117
[1] 118
[1] 119
[1] 120
[1] 121
[1] 122
[1] 123
[1] 124
[1] 125
[1] 126
[1] 127
[1] 128
[1] 129
[1] 130
[1] 131
[1] 132
[1] 133
[1] 134
[1] 135
[1] 136
[1] 137
[1] 138
[1] 139
[1] 140
[1] 141
[1] 142
[1] 143
[1] 144
[1] 145
[1] 146
[1] 147
[1] 148
[1] 149
[1] 150
[1] 151
[1] 152
[1] 153
[1] 154
[1] 155
[1] 156
[1] 157
[1] 158
[1] 159
[1] 160
[1] 161
[1] 162
[1] 163
[1] 164
[1] 165
[1] 166
[1] 167
[1] 168
[1] 169
[1] 170
[1] 171
[1] 172
[1] 173
[1] 174
[1] 175
[1] 176
[1] 177
[1] 178
[1] 179
[1] 180
[1] 181
[1] 182
[1] 183
[1] 184
[1] 185
[1] 186
[1] 187
[1] 188
[1] 189
[1] 190
[1] 191
[1] 192
[1] 193
[1] 194
[1] 195
[1] 196
[1] 197
[1] 198
[1] 199
[1] 200
[1] 201
[1] 202
[1] 203
[1] 204
[1] 205
[1] 206
[1] 207
[1] 208
[1] 209
[1] 210
[1] 211
[1] 212
[1] 213
[1] 214
[1] 215
[1] 216
[1] 217
[1] 218
[1] 219
[1] 220
[1] 221
[1] 222
[1] 223
[1] 224
[1] 225
[1] 226
[1] 227
[1] 228
[1] 229
[1] 230
[1] 231
[1] 232
[1] 233
[1] 234
[1] 235
[1] 236
[1] 237
[1] 238
[1] 239
[1] 240
[1] 241
[1] 242
[1] 243
[1] 244
[1] 245
[1] 246
[1] 247
[1] 248
[1] 249
[1] 250
[1] 251
[1] 252
[1] 253
[1] 254
[1] 255
[1] 256
[1] 257
[1] 258
[1] 259
[1] 260
[1] 261
[1] 262
[1] 263
[1] 264
[1] 265
[1] 266
[1] 267
[1] 268
[1] 269
[1] 270
[1] 271
[1] 272
[1] 273
[1] 274
[1] 275
[1] 276
[1] 277
[1] 278
[1] 279
[1] 280
[1] 281
[1] 282
[1] 283
[1] 284
[1] 285
[1] 286
[1] 287
[1] 288
[1] 289
[1] 290
[1] 291
[1] 292
[1] 293
[1] 294
[1] 295
[1] 296
[1] 297
[1] 298
[1] 299
[1] 300
[1] 301
[1] 302
[1] 303
[1] 304
[1] 305
[1] 306
[1] 307
[1] 308
[1] 309
[1] 310
[1] 311
[1] 312
[1] 313
[1] 314
[1] 315
[1] 316
[1] 317
[1] 318
[1] 319
[1] 320
[1] 321
[1] 322
[1] 323
[1] 324
[1] 325
[1] 326
[1] 327
[1] 328
[1] 329
[1] 330
[1] 331
[1] 332
[1] 333
[1] 334
[1] 335
[1] 336
[1] 337
[1] 338
[1] 339
[1] 340
[1] 341
[1] 342
[1] 343
[1] 344
[1] 345
[1] 346
[1] 347
[1] 348
[1] 349
[1] 350
[1] 351
[1] 352
[1] 353
[1] 354
[1] 355
[1] 356
[1] 357
[1] 358
[1] 359
[1] 360
[1] 361
[1] 362
[1] 363
[1] 364
[1] 365
[1] 366
[1] 367
[1] 368
[1] 369
[1] 370
[1] 371
[1] 372
[1] 373
[1] 374
[1] 375
[1] 376
[1] 377
[1] 378
[1] 379
[1] 380
[1] 381
[1] 382
[1] 383
[1] 384
[1] 385
[1] 386
[1] 387
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
Error in rbind(results_promoter_CAGE_genome, results) :
number of columns of matrices must match (see arg 2)
Calls: Gene_Centric_Noncoding_Results_Summary -> rbind
Execution halted

[yuxinyuanqt]

The log suggests this is not a global configuration issue, but a single malformed result entry.

Please run Gene_Centric_Noncoding_Results_Summary() interactively and step through the loop:

	#######################################################
	#     summarize unconditional analysis results
	#######################################################

	results_noncoding_genome <- c()

	for(kk in 1:gene_centric_noncoding_jobs_num)
	{
		print(kk)
		results_noncoding <- get(load(paste0(input_path,gene_centric_results_name,"_",kk,".Rdata")))

		results_noncoding_genome <- c(results_noncoding_genome,results_noncoding)
	}

	results_UTR_genome <- c()
	results_upstream_genome <- c()
	results_downstream_genome <- c()
	results_promoter_CAGE_genome <- c()
	results_promoter_DHS_genome <- c()
	results_enhancer_CAGE_genome <- c()
	results_enhancer_DHS_genome <- c()

	for(kk in 1:length(results_noncoding_genome))
	{
		results <- results_noncoding_genome[[kk]]
		if(is.null(results)==FALSE)
		{
			### UTR
			if(results[3]=="UTR")
			{
				results_UTR_genome <- rbind(results_UTR_genome,results)
			}
			### upstream
			if(results[3]=="upstream")
			{
				results_upstream_genome <- rbind(results_upstream_genome,results)
			}
			### downstream
			if(results[3]=="downstream")
			{
				results_downstream_genome <- rbind(results_downstream_genome,results)
			}
			### promoter_CAGE
			if(results[3]=="promoter_CAGE")
			{
				results_promoter_CAGE_genome <- rbind(results_promoter_CAGE_genome,results)
			}
			### promoter_DHS
			if(results[3]=="promoter_DHS")
			{
				results_promoter_DHS_genome <- rbind(results_promoter_DHS_genome,results)
			}
			### enhancer_CAGE
			if(results[3]=="enhancer_CAGE")
			{
				results_enhancer_CAGE_genome <- rbind(results_enhancer_CAGE_genome,results)
			}
			### enhancer_DHS
			if(results[3]=="enhancer_DHS")
			{
				results_enhancer_DHS_genome <- rbind(results_enhancer_DHS_genome,results)
			}
		}
		if(kk%%1000==0)
		{
			print(kk)
		}
	}

The error occurs at:

rbind(results_promoter_CAGE_genome, results)

So the current kk at failure is the problematic entry.
Once you have that kk, trace it back to the corresponding noncoding job file
(e.g. *Noncoding<job_id>.Rdata) and inspect its structure.