STAR and RSAM failing test on Ubuntu

[danieleottaviani]

Hi,
I installed docker4seq and rCASC. Just trying to check everything is alright by running the testSeqbox function but STAR, RSEM and annotation are keeping failing the test:

`Wed-Jun-12-15-41-04-2019
Installing the latest version of docker4seq stable release
Installing dockers images
testing RNAseq workflow
Wed-Jun-12-15-41-04-2019
testing miRNAseq
Wed-Jun-12-15-41-04-2019
testing chipseq
Wed-Jun-12-15-41-04-2019
Wed-Jun-12-15-41-04-2019
skewer passed test
STAR failed
RSEM failed
annotation by GTF failed
salmonCounts passed test
samples2experiment passed test check
sampleSize passed test
experimentPower passed test
mirnaCounts passed test
chipseqCounts passed test
Wed-Jun-12-16-01-44-2019`

If I run the star2steps function alone I get this output with error:

In your system the following version of Docker is installed:
Docker version 18.09.6, build 481bc77
creating a folder in scratch folder

copying 

setting as working dir the scratch folder and running  docker container
5c121c89f7caa5ac08d28cac8cf5ac9800d3569cbc417d3ff9d48215d6c0abf9

Docker ID is:
 5c121c89f7ca 
..........


`
Docker exit status: 0 
mv: cannot stat '/data/scratch/Wed-Jun-12-17-17-52-2019/1stpass_Log.final.out': No such file or directory
mv: cannot stat '/data/scratch/Wed-Jun-12-17-17-52-2019/2ndpass_Log.final.out': No such file or directory
sh: 1: Syntax error: Bad fd number
5c121c89f7caa5ac08d28cac8cf5ac9800d3569cbc417d3ff9d48215d6c0abf9
`

`Removing the rsemStar temporary file ....`

Error is similar with rsemstar:

`The RSEM STAR analysis is finished
mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/genes.results': No such file or directory
mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/isoforms.results': No such file or directory
mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/Log.final.out': No such file or directory
sh: 1: Syntax error: Bad fd number
3c2d386c62951b46d2e14cd02c3b9faefc0708e59c7322afb6b14371f65fec85`

Thanks for helping!
Cheers,
Daniele

`R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS`

[kendomaniac]

Dear Daniele, TestSeqbox is an old function that needs to be revised Could please tell me the characteristics of your hardware: Operative system RAM Ssd or sata disk Processor type Furthermore, After library(devtools) install_github("kendomaniac/docker4seq", ref="master") Have you done library(docker4seq) downloadContainers() And after library(devtools) install_github("kendomaniac/rCASC", ref="master") Have you done downloadContainers() Just let me kno about the abive points Please Cheers Raf Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

…

On 12 Jun 2019, at 18:31, Daniele Ottaviani ***@***.***> wrote: Hi, I installed docker4seq and rCASC. Just trying to check everything is alright by running the testSeqbox function but STAR, RSEM and annotation are keeping failing the test: Wed-Jun-12-15-41-04-2019 Installing the latest version of docker4seq stable release Installing dockers images testing RNAseq workflow Wed-Jun-12-15-41-04-2019 testing miRNAseq Wed-Jun-12-15-41-04-2019 testing chipseq Wed-Jun-12-15-41-04-2019 Wed-Jun-12-15-41-04-2019 skewer passed test STAR failed RSEM failed annotation by GTF failed salmonCounts passed test samples2experiment passed test check sampleSize passed test experimentPower passed test mirnaCounts passed test chipseqCounts passed test Wed-Jun-12-16-01-44-2019 If I run the star2steps function alone I get this output with error: ` In your system the following version of Docker is installed: Docker version 18.09.6, build 481bc77 creating a folder in scratch folder copying setting as working dir the scratch folder and running docker container 5c121c89f7caa5ac08d28cac8cf5ac9800d3569cbc417d3ff9d48215d6c0abf9 Docker ID is: 5c121c89f7ca .......... Docker exit status: 0 mv: cannot stat '/data/scratch/Wed-Jun-12-17-17-52-2019/1stpass_Log.final.out': No such file or directory mv: cannot stat '/data/scratch/Wed-Jun-12-17-17-52-2019/2ndpass_Log.final.out': No such file or directory sh: 1: Syntax error: Bad fd number 5c121c89f7caa5ac08d28cac8cf5ac9800d3569cbc417d3ff9d48215d6c0abf9 Removing the rsemStar temporary file ....` Error is similar with rsemstar: The RSEM STAR analysis is finished mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/genes.results': No such file or directory mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/isoforms.results': No such file or directory mv: cannot stat '/data/scratch//Wed-Jun-12-17-23-01-2019/Log.final.out': No such file or directory sh: 1: Syntax error: Bad fd number 3c2d386c62951b46d2e14cd02c3b9faefc0708e59c7322afb6b14371f65fec85 Thanks for helping! Cheers, Daniele R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[danieleottaviani]

Hi Raffaele,

I've got a Dell Precision M7520 workstation with Ubuntu 18.04.01 LTS installed.
Processor is Intel Xeon E3-1535M v6 (Quad Core, 8M Cache, 3.10 GHz) and have two disks (256GB PCIe SSD + 1TB SATA).
RAM is 16GB DDR4 SDRAM (2x8GB) 2400MHz Non-ECC and I should upgrade to 32GB soon.
Indeed, when I was running STAR locally I was using the flag --genomeSAsparseD 2.

Yes - I installed devtools and download containers for doker4seq and rCASC as above.

Thanks!
Best wishes,
Daniele

[kendomaniac]

Hi Daniele, For optimal working with docker4seq it would be ideal that you set the scratch folder on ssd disk. You have a nice computer, however in docker4seq Star requires about 28Gb Ram Furthermore, the star and the star/rsem index should be made using the index function provided in docker4seq. Till you upgrade to 32 Gb Ram, you can work with Salmon, which is also implemented in docker4seq. Please note that functions described in the web page are those consolidated, the other functions are still not completely mature. Thus, if you find some bug please let me know. Concerning rCASC I am revising functions help and examples, which are not as clear as I would like. Please keep posting if you need any further info Cheers Raf Prof. Raffaele A Calogero Tel +39 3333827080 Email raffaele.calogero@unito.it raffaele.calogero@gmail.com Sent from my iPhone

…

On 12 Jun 2019, at 20:31, Daniele Ottaviani ***@***.***> wrote: Hi Raffaele, I've got a Dell Precision M7520 workstation with Ubuntu 18.04.01 LTS installed. Processor is Intel Xeon E3-1535M v6 (Quad Core, 8M Cache, 3.10 GHz) and have two disks (256GB PCIe SSD + 1TB SATA). RAM is 16GB DDR4 SDRAM (2x8GB) 2400MHz Non-ECC and I should upgrade to 32GB soon. Indeed, when I was running STAR locally I was using the flag --genomeSAsparseD 2. Yes - I installed devtools and download containers for doker4seq and rCASC as above. Thanks! Best wishes, Daniele — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.