error running runSCENIC_2

[dsb66]

I am running the SCENIC pipeline in R following the instructions at https://rawcdn.githack.com/aertslab/SCENIC/0a4c96ed8d930edd8868f07428090f9dae264705/inst/doc/SCENIC_Running.html#scenic_workflow

When executing runSCENIC_2_createRegulons(scenicOptions), I obtain the following error message:

13:06 Step 2. Identifying regulons

Attaching package: ‘AUCell’

The following object is masked from ‘package:base’:

cbind

tfModulesSummary:

top5perTarget top10perTarget w005 top50perTarget top50 55 88 133 310 824 w001 884 13:06 RcisTarget: Calculating AUC Scoring database: [Source file: mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather] Error in .column_indexes_feather(x, i) : undefined columns: Pex1, 4430402I18Rik, Pi4ka, Sco2, Comtd1, Med31, Scand1, Ptges3l, Atr, AI661453, Ndufa13, Dhfr, Nusap1, Alkbh1

The sha256 checksum for my database files is correct:

70a808fb5fab0a5e97c4ab3749bb7c4610437b4140ee3ebb331b500e2a10df3d mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather ffc5eecfad00f799704737e78522c389595210ad58f3ca64fe959d78284a2323 mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather

What could be the source of this problem?

[jefferyUstc]

I encountered the same problem!

[Dongxu-Zheng]

I am running the SCENIC pipeline in R following the instructions at https://rawcdn.githack.com/aertslab/SCENIC/0a4c96ed8d930edd8868f07428090f9dae264705/inst/doc/SCENIC_Running.html#scenic_workflow When executing runSCENIC_2_createRegulons(scenicOptions), I obtain the following error message:

13:06 Step 2. Identifying regulons Attaching package: ‘AUCell’ The following object is masked from ‘package:base’: cbind

tfModulesSummary: top5perTarget top10perTarget w005 top50perTarget top50 55 88 133 310 824 w001 884 13:06 RcisTarget: Calculating AUC Scoring database: [Source file: mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather] Error in .column_indexes_feather(x, i) : undefined columns: Pex1, 4430402I18Rik, Pi4ka, Sco2, Comtd1, Med31, Scand1, Ptges3l, Atr, AI661453, Ndufa13, Dhfr, Nusap1, Alkbh1

The sha256 checksum for my database files is correct:

70a808fb5fab0a5e97c4ab3749bb7c4610437b4140ee3ebb331b500e2a10df3d mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather ffc5eecfad00f799704737e78522c389595210ad58f3ca64fe959d78284a2323 mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather

What could be the source of this problem?

@dsb66 Hi, did you solve this issue? I met the same one but had no idea on it now. Thanks for any reply or suggestions!

[dsb66]

No I never solved the issue with the mm10 database. Either the mm10__refseq-r80__10kb_up_and_down_tss file is corrupted or there is an incompatibility between the feather software version used to create the file and the one used to read it.

I simply moved back tp the mm9 files, which work without problems.

[Bodako]

Dear @s-aibar,

Hello, I have the similar problem with the hg38 database.

When I checked the sha256dsum with our database files, they were correct : fea7f9159645392970ecb2c902fb0622681dd63b9a47b36363f50569c5989f62 hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather e7f980ec2f9ddedcfc563d9ab045ea6b769eba654d3348a1fc6140b1575f9428 hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather

I obtained the following error when I ran runSCENIC_2_createRegulons:

> runSCENIC_2_createRegulons(scenicOptions)
18:14	Step 2. Identifying regulons
tfModulesSummary:

 top5perTarget           w005 top10perTarget top50perTarget          top50           w001 
           160            174            270            978           1025           1119 
18:14	RcisTarget: Calculating AUC
Error in .column_indexes_feather(x, i) : 
  undefined columns: DUS2, JMJD4, DEAF1, C1orf122, GTF3C4, PYGO2, ADAL, MED14, UTP14C, AFAP1, ARIH2, SLC5A6, CRYZ, NOP16, SNRPD3, SLC25A32

Could you comment on what would be the cause of this issue? If possible, I would like to use hg38 reference.

Thanks.

[smilesw]

I solved the problem after loading "library(data.table)" adequately. I guess that the order of library loading matters. Hope that it helps you.

Thanks

[Amz965]

Using "library(data.table)" doesn't work for me, but I try to rerun the codes about scenicOptions@settings and it works.

scenicOptions@settings$verbose <- TRUE
scenicOptions@settings$nCores <- 8
scenicOptions@settings$seed <- 123
scenicOptions@settings$dbs <- scenicOptions@settings$dbs["10kb"]

I think the problem may be the dbs is not specified, and I'm not sure whether it's the only reason of this problem.

[smilesw]

I agree with Simon6090's opinion. As mentioned in the above comment, I used mm9 as belows and it did not cause the error. The SENIC tutorial also uses mm9, not mm10.

dbs[1] <-c( "mm9-tss-centered-10kb-7species.mc9nr.feather") dbs[2] <-c( "mm9-500bp-upstream-7species.mc9nr.feather")