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federicacitarrella / FusionFlow

FusionFlow is a bioinformatic pipeline that enables the detection of gene fusions from RNA and DNA data.
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Pipeline error #24

Closed federicacitarrella closed 2 years ago

federicacitarrella commented 3 years ago

Running the pipeline I noted that the file .command.out and .command.log are discordant:

.command.out:

[EricScript] Starting EricScript analysis for sample MyEric.
[EricScript] Aligning with bwa ...done. 
[EricScript] Extracting discordant alignments ... done. 
[EricScript] Building exon junction reference ... done. 
[EricScript] Aligning to exon junction reference ... done. 
[EricScript] Recalibrating junctions ... done. 
[EricScript] Aligning to recalibrated junction reference ... done. 
[EricScript] Scoring candidate fusions ...done. 
[EricScript] Filtering candidate fusions ...done. 
[EricScript] Writing results ... done. 
[EricScript] Open /Users/federica/Desktop/pipelineGeneFusions/repo/pipelineGeneFusions/work/5a/1fc8d7c524587a6403734e02647e0f/EricScript_output/MyEric.results* to view the results of EricScript analysis.

.command.log:

[EricScript] Starting EricScript analysis for sample MyEric.
[EricScript] Aligning with bwa ...done. 
[EricScript] Extracting discordant alignments ... done. 
[EricScript] Building exon junction reference ... done. 
[EricScript] Aligning to exon junction reference ... done. 
[EricScript] Recalibrating junctions ... done. 
[EricScript] Aligning to recalibrated junction reference ... done. 
[EricScript] Scoring candidate fusions ...done. 
[EricScript] Filtering candidate fusions ...done. 
[EricScript] Writing results ... Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Calls: read.delim -> read.table
Execution halted
done. 
[EricScript] Open /Users/federica/Desktop/pipelineGeneFusions/repo/pipelineGeneFusions/work/5a/1fc8d7c524587a6403734e02647e0f/EricScript_output/MyEric.results* to view the results of EricScript analysis.

I tried to solve this error but I did not succeed.

Useful links: https://groups.google.com/g/ericscript/c/GxO1qtG8TQQ (I tried to use the command 'bwa index *.fa*' inside homo_sapiens folder, but it did not work) https://groups.google.com/g/ericscript/c/jm16SitTy2c https://groups.google.com/g/shiny-discuss/c/3qqeKyAm9nQ

Bontempogianpaolo1 commented 3 years ago

how did you solve it?

federicacitarrella commented 3 years ago

It was solved increasing the Docker container's RAM (to 16 GB).