Troubleshooting¶

Input files¶

"No biological groups were found" or a missing-column error. The sample list needs columns named exactly Injection and Sample_Code, and the metadata needs Sample_Code and Biological_Group. Check the spelling and capitalization of the header row.

Injections in the peak table are not in the sample list. Injection names must match the peak table's column headers exactly, including any date prefix or file extension your software adds. The sheet editor reads names directly from the peak table, which avoids this.

The peak table format is not recognized. Re-export with the settings in Input files. For MS-DIAL, export the alignment result (Area), not a single-sample peak list. For an unsupported program, convert the table to the Progenesis layout.

No MS2 spectra in the details panel. Upload a fragment database (.msp or .mgf) exported from the same alignment as the peak table. Spectra are matched to features by compound ID, so a fragment file from a different alignment will not line up.

Results¶

A result tab is greyed out. Result tabs open only for a completed analysis. Check the chip in the top bar; if the run failed, the Run tab shows the error in its log.

Very few features pass filtering. Look at the filtering table on Data Review to see which filter removes the most. Common causes are the wrong blank group, a relative threshold set too high, or a CV threshold too strict for a small or chemically diverse dataset.

The MS1 or MS/MS search buttons are missing. The server does not have the reference data installed. See Reference data.

A link to an analysis says it is no longer available. Analyses belong to the workspace that ran them, and old workspaces are deleted after a period of inactivity. Links do not open someone else's analysis.

Sign-in¶

The sign-in code email does not arrive. Check the spam folder. Codes expire after 15 minutes and only a few can be sent per hour, so wait before requesting another. Server operators: confirm the MPACT_SMTP_* settings and that outgoing port 587 is open.

Signed out after the site moved to a new address. Sign-ins are tied to the site's address. Sign in again; your workspace and runs are kept with your account.

Running your own server¶

fetch_reference_data.py fails with HTTP 403. npatlas.org sometimes refuses Python's default client. Download the table with curl instead and save it as npatlas.tsv in the reference directory:

curl -L -o server/data/npatlas.tsv "https://www.npatlas.org/static/downloads/NPAtlas_download.tsv"

The Docker build fails at vendor_core.py verify. A file under server/mpact_core/ differs from the pinned copy. Those files must not be edited in place; see Development. On Windows, also check that Git has not changed their line endings.

Uploads over 100 MB fail behind Cloudflare. Cloudflare's proxy limits request bodies to 100 MB on its free plan. Set the DNS record to DNS-only so uploads go straight to your server.