Hi all,
I am very naive to bioinformatics. I am using this tutorial to map a genome, but when I use multiQC tool to analyze my BAM file (MarkDuplicate Metrics) I get an error. The error is:
Fatal error: Exit code 1 ()
Tool generated the following standard error:
Module 'picard: ‘picard.analysis.AlignmentSummaryMetrics’ not found in the file 'chlamyDNA_4_S7__001_fastq’
Could anyone help me please?
Hi,
this looks like you have chosen a wrong file as your input. We have more detailed training material here, maybe that will help as well: Galaxy Training!
Ciao,
Bjoern
Hi Bjoern,
Thanks very much for your replay, but I am sure I am using the right file.I should use the file its name ends with metrics and there is only one file with that name.
In the tutorial, the tutor is mapping 4 genomes at the same time, but I am mapping only one genome. Could it cause a problem when I use MultiQC tool?
Sorry if it doesn’t make sense, I am very naive in bioinformatics.
HI @HamidGaikani,
mapping just one fastq file doesn’t explain your error. Please, could you share a screenshot of the files that you are working on in Galaxy?
Regards
Dear gallardoalba
Sorry for the late reply; I was trying to do this again, but I faced the same problem. I am attaching the screenshot. Many thanks for your help.
I did every single step exactly like the tutorial, except that I uploaded my own reference genome.
There is an open issue with the tool that appears to be what is going wrong with your example. MultiQC fails when input datasets that have the same dataset name/label -- tool issue · Issue #315 · galaxyproject/usegalaxy-playbook · GitHub
In short, when inputs share the same “name” the tool cannot accurately define/label those inputs as distinct samples when creating the report. This creates a duplicated label conflict and fails the tool.
Since your data is in a collection, try the tool Collection Operations > **Relabel List Identifiers** from contents of a file to give the inputs unique names.
Or, perhaps @bjoern.gruening @gallardoalba have a better suggestion? This wasn’t an easy problem to address during the prior tool update.
Apologies for the confusion!
Hi Jennifer,
Thanks for your kind help; much appreciated!
I will try it again and let you know about the result here.
Hi Jennifer,
This tool Relabel List Identifiers returns another error! Could I share my history with you?
If it’s possible for you to take a look…
Best,
Hamid
@HamidGaikani Sent you a direct message with instructions. Please do not delete any of the work involved (inputs or outputs or prep/intermediate steps) 
Renaming the files worked for me! Thanks a lot!
Cheers,
GG
