Problem completing the steps in the wiki

[GodloveD]

Description of the bug
I'm trying to go through the wiki here. I'm able to execute the command java -jar MSFragger.jar --config and then manually edit the closed_fragger.params file (supplying the value 2020-12-29-decoys-contam-UP000005640.fas in my case) in step 3.

But I cannot execute the next step:

$ java -Xmx32g -jar MSFragger.jar closed_fragger.params 20190202_QExHFX2_RSLC8_PST_HeLa_10ng_1ulLoop_muPAC_1hr_15k_7.raw

Because I don't have any file named *.raw. I assume that one of the steps leading to this point was supposed to have created the *.raw file? Or it did so in a previous version but no longer does so? I'm unsure.

To Reproduce
Steps to reproduce the behavior:

1. Follow the steps here.

Please complete the following information:

$ cat /etc/os-release
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

$ uname -a
Linux cn0849 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

msfragger v3.1.1
philosopher v3.3.12

Thanks!

[GodloveD]

nvrmnd. I had a another look with fresh eyes and I see that I'm supposed to download that file from anon ftp in step zero. I had thought that the download command in step one was also supposed to retrieve the *.raw file for me. Thanks.

[prvst]

I'm glad you figure it out. Please reach out to us if you need further assistance.