Need help with bwa command

[gakabani]

I apologize in advance for my lack of knowledge in bioinformatics.
I am following the Bootcamp example, and I downloaded all the files as indicated in the tutorial instructions.
Under docker, I ran the following command on page 10/59 and I am stuck.

$bwa mem -SP5M -t4 hg38.fasta input_R1.fastq input_R2.fastq | samtools view -bhS - > output.bam

The resulting output.bam file is empty (see below).

Any ideas where I am making a mistake?

The files listed in my "d" directory are as follow:

-rw-r--r-- 1 502 staff 75135953 May 11 2018 deduped.prebaked.pairsam.gz
-rw-r--r-- 1 502 staff 75455401 May 11 2018 filtered.prebaked.pairsam.gz
-rw-rw-r-- 1 500 500 17478 May 11 2018 hg38.fasta.amb
-rw-rw-r-- 1 500 500 27715 Dec 8 2016 hg38.fasta.ann
-rw-rw-r-- 1 500 500 3099922624 Dec 8 2016 hg38.fasta.bwt
-rw-rw-r-- 1 500 500 774980637 Dec 8 2016 hg38.fasta.pac
-rw-rw-r-- 1 500 500 1549961320 Dec 8 2016 hg38.fasta.sa
-rw-r--r-- 1 root root 365 May 16 2018 hg38.mainonly.chrom.size
-rw-r--r-- 1 root root 98637520 May 16 2018 input_R1.fastq
-rw-r--r-- 1 root root 91381760 May 16 2018 input_R2.fastq
-rw-r--r-- 1 root root 62 Jul 21 18:12 output.bam
-rw-r--r-- 1 502 staff 91081246 May 11 2018 output.prebaked.bam
-rw-r--r-- 1 502 staff 467041 May 11 2018 output.prebaked.cool
-rw-r--r-- 1 502 staff 1547305 May 11 2018 output.prebaked.mcool
-rw-r--r-- 1 502 staff 5222310 May 11 2018 output.prebaked.pairs.gz
-rw-r--r-- 1 502 staff 1869223 May 11 2018 output.prebaked.pairs.gz.px2
-rw-r--r-- 1 502 staff 105090651 May 11 2018 parsed.prebaked.pairsam.gz
-rw-r--r-- 1 502 staff 93158616 May 11 2018 sorted.prebaked.pairsam.gz

[pkerpedjiev]

Was there any output from the bwa command?