I am trying to run IsoEM2 in order to quantify reads in the alignment. I want to use a tool that uses an expectation maximisation method in order to cope with multi-mapped reads.

I have made sure the sam file has been sorted in the manner specified in the manual (https://github.com/mandricigor/isoem2).

My command:

isoem2 -G Reference/gencode.v34.annotation.gtf -a --directional -O Samples/Isoem_results Samples/Sample.sort.sam

However I keep getting this error:

ERROR in lineA00821:296:H37KYDSXY:2:1376:29252:7467 69  chr1    14620   0   *   =   14620   0   CCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCACAGTGCTGGTTCCATCACCCCCACCCAGGGAAGCAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAATGGCCCAAGTCTGGG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  YT:Z:UP
Exception in thread "pool-2-thread-1" java.lang.NumberFormatException: For input string: ""
    at edu.uconn.engr.dna.util.Utils.nfe(Utils.java:367)
    at edu.uconn.engr.dna.util.Utils.parseInt(Utils.java:351)
    at edu.uconn.engr.dna.util.Utils.clipSequence(Utils.java:822)
    at edu.uconn.engr.dna.isoem.processor.SamLinesToCoordParameterRunnable2.run(SamLinesToCoordParameterRunnable2.java:130)
    at edu.uconn.engr.dna.isoem.processor.SamLinesToCoordParameterRunnable2.run(SamLinesToCoordParameterRunnable2.java:23)
    at edu.uconn.engr.dna.util.BatchThreadPoolExecutor.runOne(BatchThreadPoolExecutor.java:129)
    at edu.uconn.engr.dna.util.BatchThreadPoolExecutor.runUntilQueueEmpty(BatchThreadPoolExecutor.java:124)
    at edu.uconn.engr.dna.util.BatchThreadPoolExecutor.access$100(BatchThreadPoolExecutor.java:14)
    at edu.uconn.engr.dna.util.BatchThreadPoolExecutor$ItemRunnable.run(BatchThreadPoolExecutor.java:182)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

It keeps spitting out this error with "pool-x-thread-y" increasing, and the sequence and the location changing. At the end it doesn't output any file.

Does anyone know what this error might mean or how to go about correcting it?