Error message

[snowsapiens]

When using the virtual machine provided, the process stops with the following message:

make: *** No rule to make target /data/bench/runs/neanderthal/1.sam', needed byalignment'. Stop.

Any clues concerning what might be happening?

Thanks in advance!

[wyleung]

Thanks for reporting, can you tell me how the fastq files are named?

[snowsapiens]

Thanks for replying!

The file names are:

1043_ATCACG_L005_R1_001.fastq
1043_ATCACG_L005_R2_001.fastq
1111_CGATGT_L006_R1_001.fastq
1111_CGATGT_L006_R2_001.fastq

And the rules for name-matching in the "run.sh" script are:

PEA_MARK=_R1_001
PEB_MARK=_R2_001

Thanks you advance!