R error when detecting DAS genes

[asethi-1]

Hi, I am following the tutorial using the data as explained.

When I run the DAS code:

$ liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results

I get an error presumably from R:

Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [0] Calls: colnames<- Execution halted

Any ideas how I can get around this? A student is hoping to use LIQA for her honours thesis due next week so your support would be greatly appreciated. Best wishes.

[huyustats]

Hi,

Thank you for interests in using LIQA and PennSeq.

Can you upload a sample file in list1 to facilitate my debugging?

Thanks!

[asethi-1]

Hi, I am using the example data and code in this case. However, I get the same issue with my own data. Thanks,

[asethi-1]

Hello. As a technical replicate, I installed LIQA using pip on a second machine (both running MacOS)
Again, using the example data, I can get to the 'diff' step before I am stopped by an error:

$ liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [0] Calls: colnames<- Execution halted

[bernicegu313]

I have the same question.@huyustats

Thanks!

[bernicegu313]

Hi,

Thank you for interests in using LIQA and PennSeq.

Can you upload a sample file in list1 to facilitate my debugging?

Thanks!

I have the same question

[huyustats]

Thank you for your interests in using LIQA. This bug was fixed and please upgriade LIQA to 1.1.18+. Thanks!

[bernicegu313]

Thanks for the answer @huyustats Could you provide a description of the software results file, for example, how is RelativeAbundance calculated? Thanks!

[nemitheasura]

Hi @huyustats,

I have encountered ther same error while trying to run liqa -task diff.

Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [0] Calls: colnames<- Execution halted

I also encountered following error while running liqa -task quantify:

Traceback (most recent call last): File "/usr/local/software/liqa/1.1.18/lib/python3.6/site-packages/liqa_src/quantify.py", line 153, in for read in bamFilePysam.fetch(geneChr, geneStart, geneEnd): File "pysam/libcalignmentfile.pyx", line 1082, in pysam.libcalignmentfile.AlignmentFile.fetch File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region ValueError: invalid coordinates: start (10140462) > stop (9976751)

I have the latest version of LIQA (1.1.18) with required deps installed. The errors occur while I am trying to use my own data. The analysis with provided dummy files works fine. My datafiles were checked multiple times - they are perfectly fine. The formats are ok. They were used for multiple analyses, with various tools and none of them threw an error.

Would you be so kind and provide some sort of solution?

Best regards, N.

[huyustats]

Hi @nemitheasura,

Could you upload the refgene file you used? I will check it. Thanks!

[nemitheasura]

Hi @huyustats,

you will find my refgene attached. I changed an extension to txt in order to be able to upload.

I hope that will help.

Best, N. liqa.refgene.txt

[leeei123]

I also met the same problem. When I tried to run das using my own data, it stopped by errors.

Error in optim(start, fn.opt, method = method, control = control) : initial value in 'vmmin' is not finite Error in chol.default(K) : the leading minor of order 23 is not positive definite Error in chol.default(K) : the leading minor of order 23 is not positive definite Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [0] Calls: colnames<- Execution halted

Would you be so kind and provide some sort of solution? Thanks!

[jpfry327]

I had the same issue.

The error

"Error in chol.default(K) :
the leading minor of order 23 is not positive definite"

is an error in the R package gcmr when a model fails to be constructed for a given gene. It just means that the model cannot be fit. This by itself does not cause an error in LIQA because the model construction is in a try statement, though the error text gets printed.

The script fails however, because models failed to be constructed for every gene. We get the error

'names' attribute [2] must be the same length as the vector [0]
Calls: colnames<-
Execution halted

because the final dataframe reporting the DAS results is empty, and you cannot assign column names to an empty dataframe. Thus it's a one line bug fix, but at any rate the DAS result would be empty anyway.

[rvermamsm]

I already installed gcmr package. Still, I got the same error.

sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted

Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error.

Thanks in advance.

[huyustats]

I already installed gcmr package. Still, I got the same error.

sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted

Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error.

Thanks in advance.

Hi,

it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R.

Thanks

[rvermamsm]

I tested multiple times in R. It installed properly. Still it gives me the same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats @.***> wrote:

I already installed gcmr package. Still, I got the same error. sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error. Thanks in advance.

Hi, it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R. Thanks

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[kaichop]

when you use sudo to run a software like liqa, the R installation may not be the same R installation as a user.

On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.***> wrote:

I tested multiple times in R. It installed properly. Still it gives me the same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats @.***> wrote:

I already installed gcmr package. Still, I got the same error. sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error. Thanks in advance.

Hi, it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R. Thanks

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[rvermamsm]

Thank you for your response. It works without sudo but now it generated another error.

liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted

I checked my input 1, it is not empty.

Kindly give your insight. I will be grateful for your help.

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.***> wrote:

when you use sudo to run a software like liqa, the R installation may not be the same R installation as a user.

On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.***> wrote:

I tested multiple times in R. It installed properly. Still it gives me the same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats @.***> wrote:

I already installed gcmr package. Still, I got the same error. sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error. Thanks in advance.

Hi, it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R. Thanks

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[rvermamsm]

I resolved my last query but now I got a new error. Please give your insight.

liqa -task diff -condition_1 list1 -condition_2 list2 -out controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.***> wrote:

Thank you for your response. It works without sudo but now it generated another error.

liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted

I checked my input 1, it is not empty.

Kindly give your insight. I will be grateful for your help.

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.***> wrote:

when you use sudo to run a software like liqa, the R installation may not be the same R installation as a user.

On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.***> wrote:

I tested multiple times in R. It installed properly. Still it gives me the same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats @.***> wrote:

I already installed gcmr package. Still, I got the same error. sudo liqa -task diff -condition_1 estimation/control_isoform_exp ression_estimates -condition_2 estimation/treatment_isoform_expression_estimates -out ./control_treatment_result [sudo] password for rverma: Error in library("gcmr") : there is no package called ‘gcmr’ Execution halted Could you please tell me what is wrong. should I run this command in R? If not, why it shows this error. Thanks in advance.

Hi, it seems that you did not install gcmr successfully. Please make sure gcmr successfully installed by testing library(gcmr) in R. Thanks

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[huyustats]

I resolved my last query but now I got a new error. Please give your insight. liqa -task diff -condition_1 list1 -condition_2 list2 -out controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA … On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like liqa, the R installation may not > be the same R installation as a user. > > On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.> wrote: > > > I tested multiple times in R. It installed properly. Still it gives me > the > > same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > @.> wrote: > > > > I already installed gcmr package. Still, I got the same error. > > sudo liqa -task diff -condition_1 estimation/control_isoform_exp > > ression_estimates -condition_2 > > estimation/treatment_isoform_expression_estimates -out > > ./control_treatment_result [sudo] password for rverma: Error in > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > Could you please tell me what is wrong. should I run this command in R? > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > it seems that you did not install gcmr successfully. Please make sure > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks > > > > —Reply to this email directly, view it on GitHub, or unsubscribe.You are > > receiving this because you commented.Message ID: @.> > > > > — > > Reply to this email directly, view it on GitHub > > <#5 (comment)>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > > > > . > > You are receiving this because you are subscribed to this thread.Message > > ID: @.> > > > > — > Reply to this email directly, view it on GitHub > <#5 (comment)>, or > unsubscribe > https://github.com/notifications/unsubscribe-auth/A7DUJUON5DFX2ARIWEXKJHDXAYUPZANCNFSM45CKUC5Q > . > You are receiving this because you commented.Message ID: > @.***> >

Hi, the issue maybe still from input file. I will have a test on the code.

Thanks

[rvermamsm]

Yes, please look into it and let me know as soon as possible.

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 10:28 AM huyustats @.***> wrote:

I resolved my last query but now I got a new error. Please give your insight. liqa -task diff -condition_1 list1 -condition2 list2 -out controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA … <#m-3011887697266697994_> On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like liqa, the R installation may not > be the same R installation as a user. >

On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.> wrote: > > > I tested multiple times in R. It installed properly. Still it gives me > the > > same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > @.> wrote: > > > > I already installed gcmr package. Still, I got the same error. > > sudo liqa -task diff -condition_1 estimation/control_isoform_exp

ression_estimates -condition_2 > > estimation/treatment_isoform_expression_estimates -out > > ./control_treatment_result [sudo] password for rverma: Error in > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > Could you please tell me what is wrong. should I run this command in R? > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > it seems that you did not install gcmr successfully. Please make sure > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks >

—Reply to this email directly, view it on GitHub, or unsubscribe.You are > > receiving this because you commented.Message ID: @.*> > > > > — Reply to this email directly, view it on GitHub > > <#5 (comment) https://github.com/WGLab/LIQA/issues/5#issuecomment-1504512639>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q

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Hi, the issue maybe still from input file. I will have a test on the code.

Thanks

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[rvermamsm]

I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error :

"Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted"

Could you please suggest a solution? Am I doing something wrong?

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 1:16 PM Rashi verma @.***> wrote:

Yes, please look into it and let me know as soon as possible.

Thanks & Regards

Rashi (Ph.D.)

Post-Doctoral Fellow

Neuroscience Institute

Morehouse School of Medicine

720 Westview Dr SW,

Atlanta, Georgia, USA

On Wed, Apr 12, 2023 at 10:28 AM huyustats @.***> wrote:

I resolved my last query but now I got a new error. Please give your insight. liqa -task diff -condition_1 list1 -condition2 list2 -out controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in chol.default(K) : the leading minor of order 13 is not positive definite Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA … <#m-7848516770490451371m-3011887697266697994_> On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like liqa, the R installation may not > be the same R installation as a user. >

On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.*> wrote: > > > I tested multiple times in R. It installed properly. Still it gives me > the

same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > @.*> wrote: > > > > I already installed gcmr package. Still, I got the same error. > > sudo liqa -task diff -condition_1 estimation/control_isoform_exp > > ression_estimates -condition_2 > > estimation/treatment_isoform_expression_estimates -out > > ./control_treatment_result [sudo] password for rverma: Error in > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > Could you please tell me what is wrong. should I run this command in R? > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > it seems that you did not install gcmr successfully. Please make sure > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks >

—Reply to this email directly, view it on GitHub, or unsubscribe.You are > > receiving this because you commented.Message ID: @.*> > > > > — > > Reply to this email directly, view it on GitHub > > <#5 (comment) https://github.com/WGLab/LIQA/issues/5#issuecomment-1504512639>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q

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Hi, the issue maybe still from input file. I will have a test on the code.

Thanks

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[huyustats]

I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA … On Wed, Apr 12, 2023 at 1:16 PM Rashi verma @.> wrote: Yes, please look into it and let me know as soon as possible. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at 10:28 AM huyustats @.> wrote: > I resolved my last query but now I got a new error. Please give your > insight. liqa -task diff -condition_1 list1 -condition2 list2 -out > controlDAStreatment DAS testing: Gene PSMB3 being processed...Error in > chol.default(K) : the leading minor of order 13 is not positive definite > Error in chol.default(K) : the leading minor of order 13 is not positive > definite Error in if (grepl("Error", fit.H0) == T) { : the condition has > length > 1 Execution halted Thanks & Regards Rashi (Ph.D.) Post-Doctoral > Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr > SW, Atlanta, Georgia, USA > … <#m-7848516770490451371m-3011887697266697994_> > On Wed, Apr 12, 2023 at 10:02 AM Rashi verma @.> wrote: Thank you for > your response. It works without sudo but now it generated another error. > liqa -task diff -condition_1 > ../estimation/control_isoform_expression_estimates -condition_2 > ../estimation/treatment_isoform_expression_estimates -out > controlDAStreatment Error in read.table(input.file[1]) : no lines available > in input Execution halted I checked my input 1, it is not empty. Kindly > give your insight. I will be grateful for your help. Thanks & Regards Rashi > (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of > Medicine 720 Westview Dr SW, Atlanta, Georgia, USA On Wed, Apr 12, 2023 at > 12:20 AM Kai Wang @.> wrote: > when you use sudo to run a software like > liqa, the R installation may not > be the same R installation as a user. > > > On Tue, Apr 11, 2023 at 11:17 PM rvermamsm @.> wrote: > > > I > tested multiple times in R. It installed properly. Still it gives me > the > > > same error.Sent from my iPhoneOn 11-Apr-2023, at 6:12 PM, huyustats > > > @.> wrote: > > > > I already installed gcmr package. Still, I got the > same error. > > sudo liqa -task diff -condition_1 > estimation/control_isoform_exp > > ression_estimates -condition_2 > > > estimation/treatment_isoform_expression_estimates -out > > > ./control_treatment_result [sudo] password for rverma: Error in > > > library("gcmr") : there is no package called ‘gcmr’ Execution halted > > > Could you please tell me what is wrong. should I run this command in R? > > If > > not, why it shows this error. > > Thanks in advance. > > > > Hi, > > > it seems that you did not install gcmr successfully. Please make sure > > gcmr > > successfully installed by testing library(gcmr) in R. > > Thanks > > > > > —Reply to this email directly, view it on GitHub, or unsubscribe.You > are > > receiving this because you commented.Message ID: @.> > > > > > — > > Reply to this email directly, view it on GitHub > > <#5 (comment) > <#5 (comment)>>, or > > > unsubscribe > > < > > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > https://github.com/notifications/unsubscribe-auth/ABNG3OFIL763DFOAO3HWM5TXAYNDFANCNFSM45CKUC5Q > > > > > . > > You are receiving this because you are subscribed to this > thread.Message > > ID: @.> > > > > — > Reply to this email directly, > view it on GitHub > <#5 (comment) > <#5 (comment)>>, or > > unsubscribe > > https://github.com/notifications/unsubscribe-auth/A7DUJUON5DFX2ARIWEXKJHDXAYUPZANCNFSM45CKUC5Q > > . > You are receiving this because you commented.Message ID: > @.> > > > > Hi, the issue maybe still from input file. I will have a test on the code. > > Thanks > > — > Reply to this email directly, view it on GitHub > <#5 (comment)>, or > unsubscribe > https://github.com/notifications/unsubscribe-auth/A7DUJUM7NR3LKBCQFAZSVZDXA23YJANCNFSM45CKUC5Q > . > You are receiving this because you commented.Message ID: > @.> >

Hi,

There is no error message on my current PC. I will test it on another server and get back to you.

Thanks, Yu

[doshirLV]

Hello WGLab Devlopers, a couple of bumps for this thread,

Issue 1:

Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA

I am currently running into this same error when running LIQA on my own data.

Error in read.table(input.file[1]) : no lines available in input
Execution halted

@rvermamsm How did you solve it?

Issue 2:

I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA

When running LIQA on the test data, I am also running into a similar error Rashi has been having:

DAS testing: Gene BACE2 being processed...Error in if (grepl("Error", fit.H0) == T) { 
    :the condition has length > 1
Execution halted

@huyustats Any suggestions as to what may be going on?

Much appreciated, Raj

[huyustats]

Hello WGLab Devlopers, a couple of bumps for this thread,

Issue 1:

Thank you for your response. It works without sudo but now it generated another error. liqa -task diff -condition_1 ../estimation/control_isoform_expression_estimates -condition_2 ../estimation/treatment_isoform_expression_estimates -out controlDAStreatment Error in read.table(input.file[1]) : no lines available in input Execution halted I checked my input 1, it is not empty. Kindly give your insight. I will be grateful for your help. Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA

I am currently running into this same error when running LIQA on my own data.

Error in read.table(input.file[1]) : no lines available in input
Execution halted

@rvermamsm How did you solve it?

Issue 2:

I also run example data mentioned in a tutorial on github "WGLab/LIQA: Long-read Isoform Quantification and Analysis (github.com) https://github.com/WGLab/LIQA". It has shown the same error : "Error in if (grepl("Error", fit.H0) == T) { : the condition has length > 1 Execution halted" Could you please suggest a solution? Am I doing something wrong? Thanks & Regards Rashi (Ph.D.) Post-Doctoral Fellow Neuroscience Institute Morehouse School of Medicine 720 Westview Dr SW, Atlanta, Georgia, USA

When running LIQA on the test data, I am also running into a similar error Rashi has been having:

DAS testing: Gene BACE2 being processed...Error in if (grepl("Error", fit.H0) == T) { 
    :the condition has length > 1
Execution halted

@huyustats Any suggestions as to what may be going on?

Much appreciated, Raj

Hi Raj,

Issue 1: My conclusion is the format of input condition file is wrong based on the error message. Can you provide the file you used? I will test the code based on your input.

Issue 2: There is no error when I ran the example data. I will collaborate with our lab members to run this step again to dig out the reason.

Thanks, Yu

[doshirLV]

Hello Dr. Hu,

• I believe I solved the first issue. Originally, I had listed the absolute paths of the expression estimate files which were located in a completely different folder. But, then I made an estimation subfolder containing the files I needed within the directory where I am trying to the run the script which worked.
• But there is still the same "condition has length > 1" error when running the diff task with my data and the test data.

DAS testing: Gene TMEM229B being processed...Error in while (testhalf & stepFactor < 11) { :
  missing value where TRUE/FALSE needed
Error in while (testhalf & stepFactor < 11) { :
  missing value where TRUE/FALSE needed
DAS testing: Gene SNRNP200 being processed...Error in if (grepl("Error", fit.H0) == T) { :
  the condition has length > 1
Execution halted

Hopefully this can get resolved soon, Raj

[agouru55]

Hi Raj, sorry for the delayed response. I ran this example data, like Dr. Hu did and I did not seem to run into any error. If you are still having problems, you send your input file so I can evaluate what's wrong?

[doshirLV]

Hello Anagha,

No problem. I do not need to use the diff task for my project so I do not need assistance regarding this anymore. However, I am not sure if this issue is still prevalent or if it has been fixed in the latest installation of LIQA.

Cheers, Raj