wrosan

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wrosan
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  • Thank you so much for pointing out my file path. I use virtual box and share the folder between it. So, i was actually giving a path that is in windows but linux uses a different path to access the shared files. However, after fixing the path I got…
  • @Geraldine_VdAuwera I got a suggestion to use tail command for my aligned.sam file and found out that SAM files was corrupted. Now, I am trying to redo the alignment from the start. However, I was wondering if I could use the commands, '--outSAMatt…
  • @Geraldine_VdAuwera I actually tried that too and got the same error message: Caused by: htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File 2Aligned.out.sam; Line 396 Line: NB500921:39:HK5VYBGXX:1:11309:16590:5…
  • @yasinkaymaz Looks like I copied the same error message for both of my commands. Actually I had different error message when I used Picard AddOrReplaceReadGroups options for the SAM files. The error message is: Exception in thread "main"…
  • Hi GATK team, I am trying to run this pipeline to call variant in my RNAseq data. I got my sam files from STAR aligner. However, when I try to addorreplacegroups using PICARD I get the following error message: Exception in thread "main" …