Bam file DNE

[ashleethomson]

Hi, hoping I can get some help with an error that keeps popping up when running CICERO through docker.

ERROR: Bamfile '../starfusion/Aligned.out.bam' DNE

I used STAR to generate the BAM file, and I've tried different BAM files in different locations, both sorted and unsorted, but I keep receiving this error. I'm assuming DNE means Does Not Exist. I can't actually find any official documentation regarding it. First-time CICERO user so hoping it's a simple fix. Any advice would be much appreciated and thanks in advance!

[adthrasher]

Can you share the full command you are using to invoke CICERO? It appears that you are providing a local path, which is unavailable in the container.

[ashleethomson]

Oh ok, then that's probably the issue haha. I'm currently working on a Google Cloud VM.

docker run -v CICERO-output:/reference stjude/cicero:1.4.0 Cicero.sh [-n 8] -b ../starfusion/Aligned.out.bam -g ../reference-GRCh38/Homo_sapiens/GRCh38_no_alt -r ../reference-GRCh38/Homo_sapiens/GRCh38_no_alt -o CICERO-output [-j ../starfusion/Chimeric.out.junction] [-p true] [-s 2] [-t 200000] [-c 3]

[adthrasher]

With Docker, you need to provide mount instructions to make the local paths available inside the container. These are specified with the -v argument to docker. You also don't want to include the brackets ([]) for the arguments, that just specifies that the arguments are optional.

Your command would look something like this where reference_dir, starfusion_dir, and output_dir are replaced with the appropriate paths on your file system.

docker run -v reference_dir:/reference -v starfusion_dir:/starfusion -v output_dir:/CICERO-output stjude/cicero:1.4.0 Cicero.sh -n 8 -b /starfusion/Aligned.out.bam -g GRCh38_no_alt -r /reference -o /CICERO-output -j /starfusion/Chimeric.out.junction -p -s 2 -t 200000 -c 3

[ashleethomson]

Thank you! I thought it might be something simple like that. I'm still new to Docker as well. Very much appreciate the help!