NGSrich error

[tahamasoodi]

Hi all,

I just started to use NGSrich, it seems a good tool. While trying to use it, I'm getting the following error:

Exception in thread "main" java.util.NoSuchElementException: No line found

The syntax i use is:
java NGSrich evaluate -r /home/taha/Desktop/BAM/Dau-5.bam -u hg19 -a /home/taha/Desktop/BAM/refGene.txt -t /home/taha/Desktop/BAM/TargetSeq_exome_target_regions_hg19.bed

Can anybody help?

[tahamasoodi]

Is anybody there who also come across an issue like this? Here is the full error details:


STEP 1 successfully completed

======================2======================
>>> STEP 2: computing target coverage data

/home/taha/Desktop/BAM/Dau-5.bam
/tmp/Sample_From_9_52_59_1354344779753/NGSrich_target_taha-MacPro.bed
/tmp/Sample_From_9_52_59_1354344779753/NGSrich_genome_taha-MacPro.txt
Exception in thread "main" java.util.NoSuchElementException: No line found
at java.util.Scanner.nextLine(Scanner.java:1533)
at _main.EnrichmentStatsComputer.init(EnrichmentStatsComputer.java:287)
at _main.EnrichmentStatsComputer.<init>(EnrichmentStatsComputer.java:241)
at _main.Enrichment.computeTargetCoverageFiles(Enrichment.java:305)
at _main.NGSrichEvaluate.evaluate(NGSrichEvaluate.java:285)
at NGSrich.main(NGSrich.java:48)

[tahamasoodi]

Hi,

I could run it now successfully with old version but i'm not getting the html file containing the report statistics. I just get 2 output folders (data and plot) in which plot folder is always empty. May i know where i'm wrong? Here is the syntax:

java NGSrich evaluate -r /media/Disk-2/SAM/7C_Trim/7c_210312_R12.sam -u hg19 -t /home/taha/Desktop/BAM/TargetSeq_exome_target_regions_hg19.bed -g /home/taha/Desktop/Temp/refGene.txt -s Dau -T /home/taha/Desktop/Temp/ -o /home/taha/Desktop/Report/sample

Is anyone who has experience with this?