What is "Error in value[[3L]](cond) : 'asBam' failed to open SAM/BAM file"

Question

[rj.innet]

I am encountering the below error message while creating bampaths in systemPipeR workflow running in the RStudio.

   > bampaths <- runCommandline(args=args)
  Error in value[[3L]](cond) : 'asBam' failed to open SAM/BAM file

     file: '/home/rna/sample/results/SRR446028_1.fastq.gz.hisat.sam'
      SAM file: '/home/rna/sample/results/SRR446028_1.fastq.gz.hisat.sam'
    In addition: Warning message:
    In system2(command, args = commandargs, stdout = TRUE, stderr = TRUE) :
      running command ''/home/rna/tool/hisat2-2.1.0' -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/rna/sample/results/SRR446028_1.fastq.gz.hisat.sam /home/rna/sample/data/tair10.fasta -U /home/rna/sample//home/rna/sample/data/SRR446028_1.fastq.gz /home/rna/sample/ 2>&1' had status 126

What is this [[3L]] (cond).... error?? Any suggestions to solve this error will be very helpful. Thanks!!

[ATpoint]

As people already suggested in your previous post about bowtie2, do yourself a favor and run bash commands via the command line, rather than from inside R. It only adds unnecessary complication.

[cpad0112]

exit status: 126 for “command not executable". See if you can execute in shell:

/home/rna/tool/hisat2-2.1.0 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/rna/sample/results/SRR446028_1.fastq.gz.hisat.sam /home/rna/sample/data/tair10.fasta -U /home/rna/sample//home/rna/sample/data/SRR446028_1.fastq.gz /home/rna/sample/ 2>&1

Check if hisat is executable.

[rj.innet]

I have ran the following command and it gave me the result shown below.

hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/rna/sample/results/SRR446027_1.fastq.gz.hisat.sam /home/rna/sample/data/tair10.fasta -U /home/rna/sample/data/SRR446027_1.fastq.gz

96459 reads; of these: 96459 (100.00%) were unpaired; of these: 3968 (4.11%) aligned 0 times 92491 (95.89%) aligned exactly 1 time 0 (0.00%) aligned >1 times 95.89% overall alignment rate

I guess hisat2 is working fine but 3L error is comming when I run

bampaths <- runCommandline(args=args)