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Error in countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", : input bam file missing!!! #13

Open junjunlab opened 3 years ago

junjunlab commented 3 years ago

Hi，thank you for your great tools for m6A modification analysis，i got a problem when i use the ‘countReads' function.I got this error " Error in countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", : input bam file missing!!! ",but my bam files are in the bam folder ! Their names are "CD3.input.bam" and "RD3.m6A.bam" . The follows are my code.Thank you for your reply!

spnames = c("RD3","PRD3")

TestRun <- countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", bamFolder = "E:/Ribo-seq/test-peak/bam_file/", outputDir = "./fisherPeak", modification = "m6A", binSize = 50, threads = 10, )

gnilihzeux commented 3 years ago

I think its a configure error for 'sample name'. Mine looks like this:

PC_normal.input
PC_normal.m6A
cguetta commented 3 years ago

Hello,

I am wondering whether you solve the issue as i am having the same problem. Thanks a lot!

gnilihzeux commented 3 years ago

I think its a configure error for 'sample name'. Mine looks like this:

PC_normal.input
PC_normal.m6A

@cguetta

cguetta commented 3 years ago

Hello,

Thanks a lot for your answer.

It is not a configure error for the ‘sample name’. Without changing sample name, I managed to run it with a gtf file downloaded from GENCODE. However, i got only 15.7% successfully assigned alignments, so I would like to run it with my “own GTF file”. I also tried to use gtf file from UCSC with the same error. In addition, I have some “rat” samples, and GENCODE is only for human and mouse so at some point I will need to use gtf from other source than GENCODE.

Please, set attached a screenshot of the beginning of the GENCODE gtf file and my own GTF file (if it helps).

Finally, is there a way to use option “thread” to make the program runs faster.

Thanks a lot for your help,

Best regards,

Charlotte

Charlotte Guetta-Terrier, PhD Postdoctoral Research Associate Laboratory of Cancer Epigenetics and Plasticity Rhode Island Hospital 593 Eddy Street Providence, RI 02903 Aldrich Building, 4th Floor @.***

From: Jinwen Zhang @.> Reply-To: scottzijiezhang/MeRIPtools @.> Date: Friday, October 8, 2021 at 04:53 To: scottzijiezhang/MeRIPtools @.> Cc: cguetta @.>, Mention @.***> Subject: Re: [scottzijiezhang/MeRIPtools] Error in countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", : input bam file missing!!! (#13)

I think its a configure error for 'sample name'. Mine looks like this:

PC_normal.input

PC_normal.m6A

@cguettahttps://github.com/cguetta

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/scottzijiezhang/MeRIPtools/issues/13#issuecomment-938468045, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBEVT5G42LT6B2FFY5YFFTUF2WR3ANCNFSM4ZAKTWEA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

cguetta commented 3 years ago

Hello,

Sorry to bother you again, but I also tried to run it with different samples. At the end, I got the error message :

Fit models.

Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < iter_stop) { :

missing value where TRUE/FALSE needed

In addition: Warning message:

In .get_cds_IDX(mcols0$type, mcols0$phase) :

The "phase" metadata column contains non-NA values for features of type

stop_codon. This information was ignored.

So it did create the “Intermediate” folder, but not the other files.

Thanks a lot in advance for your help,

Best regards,

Charlotte

Charlotte Guetta-Terrier, PhD Postdoctoral Research Associate Laboratory of Cancer Epigenetics and Plasticity Rhode Island Hospital 593 Eddy Street Providence, RI 02903 Aldrich Building, 4th Floor @.***

From: Charlotte Guetta @.> Date: Friday, October 8, 2021 at 07:49 To: scottzijiezhang/MeRIPtools @.>, scottzijiezhang/MeRIPtools @.> Cc: Mention @.> Subject: Re: [scottzijiezhang/MeRIPtools] Error in countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", : input bam file missing!!! (#13)

Hello,

Thanks a lot for your answer.

It is not a configure error for the ‘sample name’. Without changing sample name, I managed to run it with a gtf file downloaded from GENCODE. However, i got only 15.7% successfully assigned alignments, so I would like to run it with my “own GTF file”. I also tried to use gtf file from UCSC with the same error. In addition, I have some “rat” samples, and GENCODE is only for human and mouse so at some point I will need to use gtf from other source than GENCODE.

Please, set attached a screenshot of the beginning of the GENCODE gtf file and my own GTF file (if it helps).

Finally, is there a way to use option “thread” to make the program runs faster.

Thanks a lot for your help,

Best regards,

Charlotte

Charlotte Guetta-Terrier, PhD Postdoctoral Research Associate Laboratory of Cancer Epigenetics and Plasticity Rhode Island Hospital 593 Eddy Street Providence, RI 02903 Aldrich Building, 4th Floor @.***

From: Jinwen Zhang @.> Reply-To: scottzijiezhang/MeRIPtools @.> Date: Friday, October 8, 2021 at 04:53 To: scottzijiezhang/MeRIPtools @.> Cc: cguetta @.>, Mention @.***> Subject: Re: [scottzijiezhang/MeRIPtools] Error in countReads(samplenames = spnames, gtf = "./mm10.ncbiRefSeq.gtf", : input bam file missing!!! (#13)

I think its a configure error for 'sample name'. Mine looks like this:

PC_normal.input

PC_normal.m6A

@cguettahttps://github.com/cguetta

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/scottzijiezhang/MeRIPtools/issues/13#issuecomment-938468045, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBEVT5G42LT6B2FFY5YFFTUF2WR3ANCNFSM4ZAKTWEA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

gnilihzeux commented 3 years ago

@cguetta I used the GENCODE too. I don't understand that 15.7% successfully assigned alignments, did it strand for mapping rate ? But it has nothing to do with this software, it should do with your preprocess with your fastq files.

I've never had that error 

Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < iter_stop) { :

  missing value where TRUE/FALSE needed

Sorry, I can not help

About theads, it's actually right there. I think you should take a closer look at the manul.