Question: Iterative Mapping -> open: No such file or directory
0
stoyan.velkov • 10 wrote:
Hi, when I try running "Iterative Mapping" I get the following error. Please help!
Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]
Options: -n sort by read names
-r attach RG tag (inferred from file names)
-u uncompressed BAM output
-f overwrite the output BAM if exist
-1 compress level 1
-R STR merge file in the specified region STR [all]
-h FILE copy the header in FILE to <out.bam> [in1.bam]
Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users
must provide the correct header with -h, or uses Picard which properly maintains
the header dictionary in merging.
open: No such file or directory
[bam_sort_core] fail to open file /galaxy-repl/main/jobdir/020/446/20446985/working/combine.bam
open: No such file or directory
[main_samview] fail to open "sorted.bam" for reading.
rm: cannot remove ‘/galaxy-repl/main/jobdir/020/446/20446985/working/combine.bam’: No such file or directory
rm: cannot remove ‘/galaxy-repl/main/jobdir/020/446/20446985/working/sorted.bam’: No such file or directory
