Error in step 1

[Bella Borrero]

Running the masterscript.sh on the hpc and encountering this error: 

Step 0.1: Checking for the presence of the checkpoint file.

        The file 'checkpoints' does not exist in the input directory, creating...

Exception in thread "main" java.lang.NumberFormatException: For input string: (here is the direct file path to my reads, didnt want to include for privacy)

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

        at java.lang.Integer.parseInt(Integer.java:569)

        at java.lang.Integer.parseInt(Integer.java:615)

        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:431)

        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80) 

[Sam Westreich]

Hi Bella,

From the look of this, it's failing at step 1, where it runs Trimmomatic on the input reads.  The master_script.sh is looking for reads with a format of $INPUT_DIR/*R1*q ; there have been similar issues in the past where input files didn't have R1 and R2 in the names to designate forward and reverse reads.

Can you check the input file names to see if this is causing the issue?

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus

https://www.dnanexus.com