migmap

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Everytime I try to run migmap on fastq files generated from pandaseq I get the following error WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by...

aroederer

Infinite Loop on Processed and Exception: multiply()

2

Hello, I can't get complete output using migmap. loaded 134085 reads. Processed 133598 reads, is Infinite Loop. So my output is incomplete. Could you please help me correct this bug!...

Chuang1118

### Executing the following MiGMAP command ``` /foo/jdk1.8.0_311/bin/java \ -jar /foo/MiGMAP/migmap-1.0.3/migmap-1.0.3.jar \ --blast-dir /foo/igblast_1.4.0_binaries/ \ --custom-database /foo/MiGMAP/MiGMAP_reference_DB2_refs_humanized.txt \ --all-alleles \ --allow-incomplete \ --allow-no-cdr3 \ --allow-noncanonical \ --details fr1nt,cdr1nt,fr2nt,cdr2nt,fr3nt,fr4nt,contignt,fr1aa,cdr1aa,fr2aa,cdr2aa,fr3aa,fr4aa,contigaa \ -q...

LukeHebert

Error message when running Migmap with -R set to TRA,TRB,TRG,TRD

2

I'm getting the following when running Migmap with -R set to TRA,TRB,TRG,TRD: java.lang.IllegalArgumentException: multiply() should be called with a number of 0 or greater not: -91 [StackTrace-Short] I have attached...

Zoites

I am running migmap on bulk RNASeq data from tumour biopsies in a conda environment and I have encountered the following error with `com.antigenomics.migmap.Correct` during post-processing. When I run `com.antigenomics.migmap.Correct`...

Jack-Feltham

String index out of Bounds Exception with input fasta.

1

I am getting a string index out of bounds exception with migmap-1.0.2. Here's the error: ``` Exception in thread "Thread-14" java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.charAt(String.java:658) at...

anoronh4

How to use migmap on non-model species?

1

Hi I'd like to use migmap on bovine sequences. There is now a bovine reference database for IGH available on IMGT and I have successfully called it with a standalone...

sonalhenson

Hello, It would be extremely helpful to add the entire queried sequence to the output of the tool. Thanks

HLAmolec

Hi, I want to know is there any option able to add each cdr3's original name in the fasta to the final output? I mean if the name of the...

Meng0625

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?...

HLAmolec