LUMPY and "read only" system

usegalaxy.eu support
1

Anyone else having those issues at the moment?

Hat jemand eine Lösung?

Speziell Band führen diesen Fehler fort zur Zeit. Bei sharing und Bearbeitung durch Tools wie z.b.: LUMPY.

Meine Bams haben Reads. Keine Datei funktioniert regulär, seit ungefähr 2-3 Wochen.

Danke für eine Hilfestellung.

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout
[E::hts_open_format] Failed to open file “/tmp/collate18.0000.bam” : Read-only file system
samtools collate: Cannot open intermediate file “/tmp/collate18.0000.bam”: Read-only file system
samblaster: Loaded 195 header sequence entries.
samblaster: No reads in input SAM file.

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Does anyone have a solution?

Specifically, the software I’m using is currently exhibiting this error, particularly during sharing and processing with tools like LUMPY.

My BAM files contain reads. No file has been working correctly for about 2-3 weeks.

Thank you for any assistance.

Welcome @keykey001

Yes, that part of the message is referring to the BAM file not having any reads passing through to the output. Meaning, the tool sees a “header only” BAM file.

Since this is a forum focused discussing the Galaxy Project’s ecosystem https://galaxyproject.org/, I’m not sure if you are asking your question in the right place.

Are you working with your own Galaxy server and having problems with tool development? Do you want to explain more about this part? Are you using Planemo for development yet? https://planemo.readthedocs.io/

Or, is this all on the command line running your own tools? Do you think there is a problem with a specific version of Lumpy? If either of these, you’ll have better luck getting advice if you reach out where others doing development this way are talking. They’ll also probably need more details about your configuration re versions and things like that.

Let us know! :slight_smile: