processing different number of reads each time the same command is executed with same fasta

[HLAmolec]

Hello,

Each time I'm analyzing the same fasta file with the same parameters the number of reads processed is different. Do you have any suggestion how to fix this issue?

Thanks

Here is the command:
my $cd3 = java -jar /home/igblast/migmap-1.0.3/migmap-1.0.3/migmap-1.0.3.jar --blast-dir /home/igblast/ncbi-igblast-1.12.0/bin/ -R IGH -S human --allow-incomplete --allow-no-cdr3 --allow-noncanonical --allow-noncoding -q 1 --by-read --report $report $fasta $migmap;

Here is the exception thread:

Exception in thread "Thread-16" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:197)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
Exception in thread "Thread-12" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:195)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
Exception in thread "Thread-13" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:195)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
Exception in thread "Thread-14" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:195)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
Exception in thread "Thread-10" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:195)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
[Wed Jun 05 12:21:46 EDT 2019 MIGMAP +00m13s] Loaded 8230 reads. Processed 1087 reads, of them 99.63% mapped. Among mapped reads 99.9% passed quality filter and 99.9% passed all filters.
Exception in thread "Thread-15" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:199)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
Exception in thread "Thread-11" java.lang.NullPointerException
at org.codehaus.groovy.runtime.DefaultGroovyMethods.getAt(DefaultGroovyMethods.java:7162)
at com.antigenomics.migmap.blast.BlastParser.createAlignment(BlastParser.groovy:59)
at com.antigenomics.migmap.blast.BlastParser.parse(BlastParser.groovy:197)
at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:209)
at com.antigenomics.migmap.pipeline.Pipeline$2.run(Pipeline.groovy:84)
at java.base/java.lang.Thread.run(Thread.java:834)
[Wed Jun 05 12:21:48 EDT 2019 MIGMAP +00m15s] Finished analysis. Processed 1766 reads, of them 99.6% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.