picard FastqToSam is giving me "File not found"

Question

[dwturnell63]

when i run the following:

~ $picard FastqToSam \

F1=usr/local/Cellar/picard-tools/2.22.3/bin/untrimmed_reads.fastq \

O=unaligned_reads.bam \

SM=sample001 \

RG=r0013

I get

-bash: F1=usr/local/Cellar/picard-tools/2.22.3/bin/untrimmed_reads.fastq: No such file or directory

Running

~ $picard FastqToSam -h

gets me the help screen.

changing my directory and running

java -jar picard.jar FastqToSam \

F1=usr/local/Cellar/picard-tools/2.22.3/bin/untrimmed_reads.fastq \

O=unaligned_reads.bam \

SM=sample001 \

RG=r0013

Also, doesn't work.

What am I doing wrong? The file exists!

[dwturnell63]

Figured it out. problem two was my issue. This is the first time I've ever messed with anything more then python scripts and I didn't realize how different usr is from user.

Answer 1

[Pierre Lindenbaum]

1) what is the output of

ls usr/local/Cellar/picard-tools/2.22.3/bin/untrimmed_reads.fastq

and

ls /usr/local/Cellar/picard-tools/2.22.3/bin/untrimmed_reads.fastq

2) what a bad place to put this untrimmed_reads.fastq.