David Zhang

Using the Ubuntu with the SWAN preinstalled:

We have run the swan_stat successfully: $SWAN_BIN/swan_stat /home/user/SWAN_test/P26-13.bam

However encountered errors when attempting to run the following swan_scan command: $SWAN_BIN/swan_scan -c a -n /home/user/R/x86_64-pc-linux-gnu-library/3.2/swan/data/human_g1k_v37.fasta.gap.bed /home/user/SWAN_test/human_g1k_v37.fasta /home/user/SWAN_test/P26-13.bam

The error message output: Error in scanFa(ref, param = scanFaIndex(ref)) : error in evaluating the argument 'param' in selecting a method for function 'scanFa': Error in file(file, "r") : cannot open the connection Calls: scanFaIndex -> scanFaIndex -> scan -> file Execution halted

We have tested swan_scan on the example using the provided gap ref: $SWAN_BIN/swan_scan -c a -n /home/user/R/x86_64-pc-linux-gnu-library/3.2/swan/data/human_g1k_v37.fasta.gap.bed example/example.fna example/example.lib1.bam

and tested our .bam file with the example gap and ref files: $SWAN_BIN/swan_scan -c a -n example/example.gap.bed example/example.fna example/example.lib1.bam

Both of these run fine, so we think the error is associated with our ref file. We are using human_g1k_v37.fasta as the ref file and checked the path of the file to be correct.

The ref file head: head /home/user/SWAN_test/human_g1k_v37.fasta

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

We're not sure why our .fasta ref file would be producing this error and any help would be much appreciated! Many thanks

David

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