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FastqToSam error

ac4ucsdac4ucsd United StatesMember


I am trying to generate bam files from reads (originally in fasta format) with ‘artifical Q-score’ generated with the attached script ‘fasta_to_fastq’
First step : I created fastq file from source fasta file (R1R2.fasta attached)
Second step: I am trying to convert the R1R2.fastq file to bam file (here I am using FastqToSam command below)
Final step (my goal): use the bam file as input for haploclique (

java -jar /Users/antoinechaillon/Documents/HIV/TOOLS/picard-tools-1.89/picard-tools-1.89/FastqToSam.jar F1=R1R2.fastq O=R1R2.bam SM=for_tool_testing

I get this error (screenshot)

thoughts? alternative approach?
thanks for your help ++


Issue · Github
by shlee

Issue Number
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Best Answer


  • ac4ucsdac4ucsd United StatesMember

    thank you so much!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi a,

    You can see the improved error message in the next Picard Release, or you can clone and build picard from GitHub.


  • ronlevineronlevine Lexington, MAMember ✭✭

    @ac4ucsd The error message will read name and the base's decimal and ASCII character representation.

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