all_counts.txt prints numbers instead of miRNA names

[tolarnik]

Hello,

I am using the docker4seq through the GUI to perform miRNA counting on fastq file (using mus musculus - mmu - as a reference miRBase organism). All seems to be working well, there are no errors in the log file, yet in the all_counts.txt file, there are numbers instead of miRNA names -> see attached file.

I tried the downloadContainers again and all seems to be downloaded. Any idea why this might be happening? Alternatively, is there any way to somehow cross-ling the numbers in the all_couts.txt file with a list of miRNAs?

Thank you very much
all.counts.txt

output in Routput:

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> ##First read in the arguments listed at the command line
> args=(commandArgs(TRUE))
> 
> ##args is now a list of character vectors
> ## First check to see if arguments are passed.
> ## Then cycle through each element of the list and evaluate the expressions.
> if(length(args)==0){
+     print("No arguments supplied.")
+     ##supply default values
+ }else{
+     for(i in 1:length(args)){
+       eval(parse(text=args[[i]]))
+     }
+ }
> 
> 
> library(docker4seq)
> mirnaCounts(group = group, fastq.folder =  fastq.folder, scratch.folder =  scratch.folder, mirbase.id= mirbase.id, download.status=  download.status, adapter.type= adapter.type, trimmed.fastq= trimmed.fastq)

 In your system the following version of Docker is installed:
Docker version 20.10.17, build 100c70173a30db2e3381ac0eaf2e5b67b68ffe721d68ffa8dbaec24be9d2269ef386f8c

Docker ID is:
 73a30db2e338 
..


Docker exit status: 0 

FastQC analysis is finished
het2.fastq.gz
Started analysis of het2.fastq.gz_tmp
Approx 10% complete for het2.fastq.gz_tmp
Approx 20% complete for het2.fastq.gz_tmp
Approx 30% complete for het2.fastq.gz_tmp
Approx 35% complete for het2.fastq.gz_tmp
Approx 45% complete for het2.fastq.gz_tmp
Approx 60% complete for het2.fastq.gz_tmp
Approx 70% complete for het2.fastq.gz_tmp
Approx 80% complete for het2.fastq.gz_tmp
Approx 90% complete for het2.fastq.gz_tmp
Approx 100% complete for het2.fastq.gz_tmp
Analysis complete for het2.fastq.gz_tmp
73a30db2e3381ac0eaf2e5b67b68ffe721d68ffa8dbaec24be9d2269ef386f8c


Removing the temporary file ....

 In your system the following version of Docker is installed:
Docker version 20.10.17, build 100c701
creating a folder in scratch folder

setting as working dir the scratch folder and running mirna8 docker container
e9ec05bbfecce9ca26757b6050c8382f4287dfd610665fed15b46e9b712406b1

Docker ID is:
 e9ec05bbfecc 
...................................


Docker exit status: 0 

mirnaCounts analysis is finished
sh: 1: Syntax error: Bad fd number
e9ec05bbfecce9ca26757b6050c8382f4287dfd610665fed15b46e9b712406b1


Removing the rsemStar temporary file ....
> 
> 
> 
> proc.time()
   user  system elapsed 
  3.848   1.377 355.218 ```