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HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

License: Other

Groovy 96.23% TeX 2.41% Shell 1.35%

bioinformatics ngs sequencing t-cell-receptor antibody immunology t-cell rep-seq

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xflicsu tstdk tiffany52dog yeli-bioinformatics sdwfrost al3n70rn rtobes jchenpku colindaven fenggen2016 jianqiao-shen rakeshponnala meng0625 shulp2211 tyl868 mengchengyao mqondisi

migmap's Issues

Out-of-frame

There is a rare issue with out-of-frame V-J when igblast reports N/A. Needs further investigation, perhaps should compute the frame manually in this case

Smart cache

to speed up on large datasets which are usually highly redundant
e.g. https://github.com/ben-manes/caffeine/wiki/Eviction#size-based

StringIndexOutOfBounds in Correct module

I've been using migmap for a week now, and in order to use the Analyze module, I've run my migmap output (from merged illumina reads spanning VDJ) through the MergeContigs and Correct modules. Unfortunately the Correct module seems to almost always spits out this type of error (Please see below). Is there anything I can do to fix it, or might it be a fix at your end? Please advise. I realize this is similar to an issue (#31) regarding the main migmap module which apparently was already fixed, but maybe it's a secondary issue? Thanks for your time.
Correct module invoked without additional parameters.

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 372
at java.lang.String.substring(String.java:1963)
at org.codehaus.groovy.runtime.StringGroovyMethods.getAt(StringGroovyMethods.java:1451)
at org.codehaus.groovy.runtime.dgm$1088.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure3$_closure21.doCall(Correct.groovy:132)
at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.BooleanReturningMethodInvoker.invoke(BooleanReturningMethodInvoker.java:51)
at org.codehaus.groovy.runtime.callsite.BooleanClosureWrapper.call(BooleanClosureWrapper.java:53)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4281)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4153)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4125)
at org.codehaus.groovy.runtime.dgm$205.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure3.doCall(Correct.groovy:130)
at sun.reflect.GeneratedMethodAccessor13.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.antigenomics.migmap.Correct$_run_closure4$_closure23$_closure24.doCall(Correct.groovy:154)
at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at groovy.lang.Closure.call(Closure.java:426)
at groovy.lang.Closure.call(Closure.java:442)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2056)
at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure4$_closure23.doCall(Correct.groovy:150)
at sun.reflect.GeneratedMethodAccessor16.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at groovy.lang.Closure.call(Closure.java:426)
at groovy.lang.Closure.call(Closure.java:442)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2056)
at org.codehaus.groovy.runtime.dgm$162.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct$_run_closure4.doCall(Correct.groovy:143)
at sun.reflect.GeneratedMethodAccessor18.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at groovy.lang.Closure.call(Closure.java:426)
at groovy.lang.Closure.call(Closure.java:442)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
at org.codehaus.groovy.runtime.dgm$158.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.antigenomics.migmap.Correct.run(Correct.groovy:142)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1210)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:917)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:900)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:410)
at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.antigenomics.migmap.Correct.main(Correct.groovy)

Rewrite amino acid mutation output

Use annotateMutationsAa for each clonotype instead of the formatting stuff

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

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 error log file.
_migmap_error.log

Has anyone seen this before? It is a bug?

BlastParser needs refactoring

Simplify .parse() method

How to use migmap on non-model species?

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 version of igblast. However, I am interested in the additional functionalities offered for analysing igblast output in migmap. Is there a way I can either call the bovine database for the full analysis or plugin the igblast output I've generated using the standalone igblast to do the downstream processing?

Many thanks

Reporting sequence details

CDR/FR regions and the contig

Resources optimization

Optimize segments library + IMGT/KABAT CDR/FW partitioning.
- Problem with rhesus_monkey segments
- Consider omit KABAT and simply use IMGT that is compatible with resources/segments.txt
Consider adding igblast and makeblastdb binaries to package

PrepareDatabaseNew.groovy does not create all files

Hi, when I run groovy PrepareDatabaseNew.groovy in the dataprep/ directory, most of the time not all database files are created. The .fa files are there, but makeblastdb seems to not have run for some of them. It’s not deterministic. Here is an example:

$ groovy PrepareDatabaseNew.groovy ; ls database|wc -l
90
$ groovy PrepareDatabaseNew.groovy ; ls database|wc -l
120
$ groovy PrepareDatabaseNew.groovy ; ls database|wc -l
99

When I changed the "makeblastdb ...".execute() line in the script to println "makeblastdb ...".execute().text, it started working and all 126 (in my case) expected files are created.

Command line issues

Hi,

I have tried Miniconda and the git clone versions and have got nowhere so far.

Java: java8 openjdk version "1.8.0_102"

java -Xmx8g  -jar /mnt/ngsnfs/tools/miniconda2/share/migmap.jar  -R IGH --data-dir /mnt/ngsnfs/tools/migmap/migmap/data/internal_data/ -S human in.fa

Also no luck
java -Xmx8g  -jar /mnt/ngsnfs/tools/miniconda2/share/migmap.jar  -R IGH --data-dir /mnt/ngsnfs/tools/migmap/migmap/data/ -S human in.fa

Any ideas? Any way to provoke a helpful debug msg instead of just the usage ?
usage: migmap [options] input.(fa/fastq)[.gz] (output_file/- for stdout)
--all-alleles Will use all alleles during

I presume the data files are not being found or similar. igblastn and makeblastdb are in the path.

Thanks,
Colin

SNAPSHOT

migmap-1.0.2-SNAPSHOT.jar.zip

Storing SNAPSHOT versions here

Combining incomplete reads to full clonotypes

careful consideration needed

how are reads filtered out?

Hello developers of IgBlastWrp,

I used the wrapper on a fasta file with 1000 sequences and got an output of 980 (sum of counts = 980 as well). Is it possible to know which sequences were filtered out/kept or simply avoid any filtering with the current implementation of IgBlastWrp?

For different quality parameters (-q) the same results were found as well with/without using the flag (--no-cdr3 and withough -f or -c)

BTW: what are the possible filtering criteria that lead to such a scenario?

Best

aa position reference

Migmap results show position of amino acid (pos.aa) where the changes (from.aa) occur due to somatic hypermutations to another amino acid (to.aa). I am trying to get the amino acid reference sequences for human IGH,IGL,IGK run. Please let me know how to get this done.

I require this information to quantify the number of significant somatic mutations at the amino acid level and be able to visualize it. The visualization plan is to have x axis of reference amino acid sequence and Y axis of 20 AA + stop & undetermined.

--custom-database not working

Hi,
As the title suggests, when specifying --custom-database my_segments.txt in migmap, it returns the following error:

Reproducing the error:

Downloaded IMGT/GENE-DB files
Parsed them using imgtparser - java -jar imgtparser-1.0.0.jar -nmsb human_igh.imgt out, lets assume human_igh.imgt is all that's required
java -jar migmap-1.0.1.jar --custom-database out.txt --all-alleles --allow-incomplete --allow-noncoding --allow-no-cdr3 --allow-noncanonical --blast-dir /path/to/my/blast1.4 --data-dir /path/to/my/blast1.4_data -S human -R IGH infile.fastq out
Just to make sure, I've also tried running java -jar migmap-1.0.1.jar com.antigenomics.migmap.AnnotateSegments -S human -R IGH out.txt annotated_out.txt, followed by (3) again but substituting out.txt with annotated_out.txt with no luck

I've also tried doing --custom-database segments.txt, the file that's provided in this repo here, and the same error appeared!

It would be great to see a working example (string of commands) from the raw IMGT files right down to the final segments.txt file that can be used for --custom-database.

Cheers,
Harry

Compute total count only for clonotypes that passed all filters?

Amino acids for mutations

Collapse nucleotide mutation list to amino acid mutation list

Kabat numbering not working with --details ?

./migmap --use-kabat --blast-dir /data/xxx/ncbi-igblast-1.6.1/bin --data-dir /data/xxx/migmap-1.0.2/data -R IGH -S human --by-read --details fr1aa,fr2aa,fr3aa,cdr1aa,cdr2aa test.txt test.kabat.txt
[Tue Mar 07 12:10:17 PST 2017 MIGMAP +00m00s] Loaded database for human IGH gene(s): 89 Variable, 37 Diversity and 6 Joining segments.
[Tue Mar 07 12:10:17 PST 2017 MIGMAP +00m00s] Creating temporary BLAST database /data/xxx/migmap-1.0.2/data/database-a06324d2-8746-4ea1-9bd3-35ae88c29cec.
[Tue Mar 07 12:10:17 PST 2017 MIGMAP +00m00s] Annotating variable segments.
[Tue Mar 07 12:10:19 PST 2017 MIGMAP +00m02s] Fully annotated 0 of 89 segments.
[Tue Mar 07 12:10:19 PST 2017 MIGMAP +00m02s] Analyzing sample test.txt
[Tue Mar 07 12:10:19 PST 2017 MIGMAP +00m02s] Started analysis
[Tue Mar 07 12:10:19 PST 2017 MIGMAP +00m02s] Loaded 159 reads.
[Tue Mar 07 12:10:24 PST 2017 MIGMAP +00m07s] Finished analysis. Processed 2000 reads, of them 100.0% mapped. Among mapped reads 42.2% passed quality filter and 29.8% passed all filters.
[Tue Mar 07 12:10:24 PST 2017 MIGMAP +00m07s] Finished.

./migmap -Xmx14G --blast-dir /data/xxx/ncbi-igblast-1.6.1/bin --data-dir /data/xxx/migmap-1.0.2/data -R IGH -S human --by-read --details fr1aa,fr2aa,fr3aa,cdr1aa,cdr2aa test.txt test.imgt.txt
[Tue Mar 07 12:10:54 PST 2017 MIGMAP +00m00s] Loaded database for human IGH gene(s): 89 Variable, 37 Diversity and 6 Joining segments.
[Tue Mar 07 12:10:54 PST 2017 MIGMAP +00m00s] Creating temporary BLAST database /data/xxx/migmap-1.0.2/data/database-3672583a-048e-4a01-9719-034d9c5a541d.
[Tue Mar 07 12:10:54 PST 2017 MIGMAP +00m00s] Annotating variable segments.
[Tue Mar 07 12:10:57 PST 2017 MIGMAP +00m02s] Fully annotated 89 of 89 segments.
[Tue Mar 07 12:10:57 PST 2017 MIGMAP +00m02s] Analyzing sample test.txt
[Tue Mar 07 12:10:57 PST 2017 MIGMAP +00m02s] Started analysis
[Tue Mar 07 12:10:57 PST 2017 MIGMAP +00m02s] Loaded 393 reads.
[Tue Mar 07 12:11:02 PST 2017 MIGMAP +00m07s] Finished analysis. Processed 2000 reads, of them 100.0% mapped. Among mapped reads 42.2% passed quality filter and 30.0% passed all filters.
[Tue Mar 07 12:11:02 PST 2017 MIGMAP +00m07s] Finished.

When comparing test.imgt.details to test.kabat.details , the fr1aa, fr2aa, fr3aa, cdr1aa, and cdr2aa sequences at the end of the tables are messed up (concatenated together, and seemingly wrong sequences).

IMGT on read SRR747768.2037:
XXQLVESGGGVVQPGRSLRLSCAAS MHWVRQAPGKGLEWVAV YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYY GFTFSSYG ISYDGSNK

Kabat on read SRR747768.2037:
XXAAGGVWGRRGPAWEVPETLLCSLWIHLQ*LWHALGPPGSRQGAGVGGSYII*WK**ILCRLREGPIHHLQRQFQEHAVSANEQPES*GHGCVL

test.txt
test.imgt.txt
test.kabat.txt

Stop Codons Outputting as "?"

Hi Mike,

It seems that when an alignment has a stop codon in the cdr3, the amino acid output contains a "?"

In my particular case I see something like what I've attached where the NT sequence is:
TGTGCTCTGAGTGAGGATGAAACTGGGGCAAACAACCTTTCTTT
and the AA sequence reported is:
CALSEDEa?cWGKQPFF

It seems like this was once an issue in BLAST: http://blastedbio.blogspot.com/2012/08/stop-breaking-ncbi-blast-searches.html.

Thanks,
Sam

2014-IV9-TCR-E10_S58_L001_aligned.txt

MiGMAP and MiXCR

I have read the paper "High-quality full-length immunoglobulin profiling with unique molecular barcoding" and noticed this awesome software. Just want to know what the specific feature of MiGMAP compared with MiXCR? Because our lab is currently only using MiXCR for the TCR data analysis.
Thanks!

Load clonotype table from plain-text file

Remove --write-binary mess
This will ensure compatibility with Correct and MergeContigs utils

Error correction

Based on contigs and tree map

Check bad contignt

E.g. ATCGGGGCTATTTATCCTGGAAATGGTGATACTAGTTACAATCAGAAGTTCAAGGGCAAGGCCACATTGACTGCAGACAAATCCTCC

Optimize some routines in java

Error with fasta processing

Reason: null quality for fasta records

Exception in thread "Thread-11" java.lang.NullPointerException: Cannot invoke method reverse() on null object
    at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:35)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
    at com.antigenomics.higblast.io.Read.getRc(Read.groovy:31)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.MethodMetaProperty$GetBeanMethodMetaProperty.getProperty(MethodMetaProperty.java:76)
    at org.codehaus.groovy.runtime.callsite.GetEffectivePogoPropertySite.getProperty(GetEffectivePogoPropertySite.java:85)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:307)
    at com.antigenomics.higblast.mapping.ReadMapping.<init>(ReadMapping.groovy:35)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
    at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:255)
    at com.antigenomics.higblast.blast.BlastInstance.take(BlastInstance.groovy:77)
    at com.antigenomics.higblast.blast.BlastInstance.take(BlastInstance.groovy)
    at com.antigenomics.higblast.io.OutputPort$take$0.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
    at com.antigenomics.higblast.Pipeline$2.run(Pipeline.groovy:81)
    at java.lang.Thread.run(Thread.java:745)

Read merging

Paired-end
Multi-chain

Output file

Hello,

is under the current implementation of igblastwrp possible to specify the name of the output file?

Preserving the headers of the FASTQ file in the output chart

Hi Mikhail,
How are you? My name is Rebecca and I am a Masters student studying Bioengineering.
I am trying to use your IgWrapper on FASTQ data that I have an was wondering if there is a way to keep the names of the sequences (the headers) in the output file. I have tried multiple things without success and was wondering if there is a built in way to do this.
Thank you

selectable V D and J gene

Hi Mike,
I really appreciate your Program. By showing the mutations and the number of deleted nucleotides it does exactly what I need. There is only one Problem. If Sequences are highly mutated the classification of the V, D and J gets more inaccurate. So that two Sequences which differ in only very few bases are classified as different V’s(or D’s or J’s), even if I know that those Sequences should have the same V.
So my Question is, would it be possible to analyze fastq files with a determined V D and J for all Sequences?
thanks a lot
Arved

here is an example of my problem:

Logging options & statistics

Implement statistics calculation in clonotype assembler and clonotype filter classes
Add logging option to store extraction details to file

Mutation nomenclature

Hello,
I'm having trouble relating the mutation description back to the sequence.
eg S119:A>C. I take this to mean the 119th nucleotide (after concatenating the domains) has mutated from A to C. Does the S stand for Substitution? I also see I (for Insertion perhaps?).
When I check these against the sequence the residues in the positions indicated don't always match up with what the mutation should have effected. Is there an explanation for this - some indicator somewhere implying the starting nucleotide index should be incremented somehow. Sometimes I can see that all the numbers are out 1 or 3 residues - but the rule isn't consistent across all my sequences.
Thanks in advance for any advice.

CDR3 markup reporting

Add V del, 5'3'D del and J del

Ensure that read details are stored

Read ids for clonotype
Read header for by read output

Logging

Report extraction & filtering results

StringIndexOutOfBoundsException

Command:

MIGMAP="java -Xmx50G -jar /home/registry5/apps/migmap-0.9.9/migmap-0.9.9.jar"
$MIGMAP -R IGH -S human -q 25 --allow-noncanonical --allow-incomplete  in.fastq out.migmap.tsv

Error Stack:

Exception in thread "Thread-63" java.lang.StringIndexOutOfBoundsException: String index out of range: 39
    at java.lang.String.charAt(String.java:658)
    at com.antigenomics.migmap.blast.PSegmentSearcher.searchLeft(PSegmentSearcher.groovy:80)
    at com.antigenomics.migmap.blast.PSegmentSearcher.search(PSegmentSearcher.groovy:37)
    at com.antigenomics.migmap.blast.PSegmentSearcher$search.call(Unknown Source)
    at com.antigenomics.migmap.blast.BlastInstance.createReadMapping(BlastInstance.groovy:124)
    at com.antigenomics.migmap.blast.BlastInstance.take(BlastInstance.groovy:199)
    at com.antigenomics.migmap.Pipeline$2.run(Pipeline.groovy:84)
    at java.lang.Thread.run(Thread.java:745)

It then gets stuck in loop repeating the same output.

Attached is a fastq file that produces the output. The reads are CDR3 region only, with a min nt length of 40. Help is very much appreciated as im getting this with several files.

Thanks a lot,
Joel

290test.fastq.zip

Basic tree building capabilities and mutation statistics

Provide both by-read output and assembled clonotype least in a single run

string index out of range

Hi Mike,

I've been following this project and tried using it recently since you added the --by-read option. Thank you for adding that feature! Today, I downloaded version 0.9.5 and tried playing with it. However, when I invoked it using the following command, I got the following output:

java -jar lib/higblast-0.9.5/higblast-0.9.5.jar --details all --all-alleles --allow-incomplete --allow-no-cdr3 --allow-noncanonical --allow-noncoding --by-read -S human -R IGH,IGK,IGL -p 4 -q 2 intermediate/150408-1-F3/150408-1-F3_reheader.fasta tmp/150408-1-F3_IG_higblast.tab

[Thu Sep 17 18:36:06 UTC 2015 HIGBLAST +00m00s] Loaded database for HomoSapiens IGH,IGK,IGL gene(s): 485 Variable, 44 Diversity and 32 Joining segments.
[Thu Sep 17 18:36:06 UTC 2015 HIGBLAST +00m00s] Creating temporary BLAST database /large/dkoppstein/add_conda/lib/higblast-0.9.5/data/database-4e91cee6-4342-4126-ae22-ab9b28771d7a.
[Thu Sep 17 18:36:06 UTC 2015 HIGBLAST +00m00s] Annotating variable segments.
[Thu Sep 17 18:36:28 UTC 2015 HIGBLAST +00m21s] Fully annotated 485 of 485 segments.
[Thu Sep 17 18:36:28 UTC 2015 HIGBLAST +00m21s] Analyzing sample intermediate/150408-1-F3/150408-1-F3_reheader.fasta
[Thu Sep 17 18:36:28 UTC 2015 HIGBLAST +00m21s] Started analysis
[Thu Sep 17 18:36:28 UTC 2015 HIGBLAST +00m21s] Loaded 67 reads.
[Thu Sep 17 18:36:38 UTC 2015 HIGBLAST +00m31s] Loaded 1556 reads. Processed 239 reads, of them 100.0% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:36:48 UTC 2015 HIGBLAST +00m41s] Loaded 2465 reads. Processed 903 reads, of them 100.0% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:36:58 UTC 2015 HIGBLAST +00m51s] Loaded 3373 reads. Processed 1813 reads, of them 100.0% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:37:08 UTC 2015 HIGBLAST +01m01s] Loaded 4284 reads. Processed 2725 reads, of them 99.96% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
Exception in thread "Thread-7" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
    at java.lang.String.substring(String.java:1955)
    at java_lang_String$substring$8.call(Unknown Source)
    at com.antigenomics.higblast.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getFr3nt(ReadMappingDetailsProvider.groovy:130)
    at sun.reflect.GeneratedMethodAccessor80.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:1847)
    at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:3737)
    at com.antigenomics.higblast.mapping.ReadMappingDetailsProvider$ReadMappingDetails.getProperty(ReadMappingDetailsProvider.groovy)
    at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:172)
    at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.getProperty(ScriptBytecodeAdapter.java:456)
    at com.antigenomics.higblast.mapping.ReadMappingDetailsProvider$_getDetailsString_closure3.doCall(ReadMappingDetailsProvider.groovy:65)
    at sun.reflect.GeneratedMethodAccessor75.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1019)
    at groovy.lang.Closure.call(Closure.java:426)
    at groovy.lang.Closure.call(Closure.java:442)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.collect(DefaultGroovyMethods.java:3170)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.collect(DefaultGroovyMethods.java:3140)
    at org.codehaus.groovy.runtime.dgm$66.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at com.antigenomics.higblast.mapping.ReadMappingDetailsProvider.getDetailsString(ReadMappingDetailsProvider.groovy:65)
    at com.antigenomics.higblast.mapping.ReadMappingDetailsProvider$getDetailsString.call(Unknown Source)
    at com.antigenomics.higblast.io.ReadMappingOutput.put(ReadMappingOutput.groovy:51)
    at com.antigenomics.higblast.io.ReadMappingOutput$put.call(Unknown Source)
    at com.antigenomics.higblast.Pipeline$2.run(Pipeline.groovy:97)
    at java.lang.Thread.run(Thread.java:745)
[Thu Sep 17 18:37:18 UTC 2015 HIGBLAST +01m11s] Loaded 4963 reads. Processed 3610 reads, of them 99.97% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:37:28 UTC 2015 HIGBLAST +01m21s] Loaded 5648 reads. Processed 4297 reads, of them 99.95% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:37:38 UTC 2015 HIGBLAST +01m31s] Loaded 6328 reads. Processed 4982 reads, of them 99.93% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:37:48 UTC 2015 HIGBLAST +01m41s] Loaded 6911 reads. Processed 5665 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:37:58 UTC 2015 HIGBLAST +01m51s] Loaded 6911 reads. Processed 6476 reads, of them 99.95% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:08 UTC 2015 HIGBLAST +02m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:18 UTC 2015 HIGBLAST +02m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:28 UTC 2015 HIGBLAST +02m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:38 UTC 2015 HIGBLAST +02m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:48 UTC 2015 HIGBLAST +02m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:38:58 UTC 2015 HIGBLAST +02m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:08 UTC 2015 HIGBLAST +03m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:18 UTC 2015 HIGBLAST +03m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:28 UTC 2015 HIGBLAST +03m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:38 UTC 2015 HIGBLAST +03m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:48 UTC 2015 HIGBLAST +03m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:39:58 UTC 2015 HIGBLAST +03m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:08 UTC 2015 HIGBLAST +04m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:18 UTC 2015 HIGBLAST +04m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:28 UTC 2015 HIGBLAST +04m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:38 UTC 2015 HIGBLAST +04m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:48 UTC 2015 HIGBLAST +04m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:40:58 UTC 2015 HIGBLAST +04m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:08 UTC 2015 HIGBLAST +05m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:18 UTC 2015 HIGBLAST +05m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:28 UTC 2015 HIGBLAST +05m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:38 UTC 2015 HIGBLAST +05m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:48 UTC 2015 HIGBLAST +05m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:41:58 UTC 2015 HIGBLAST +05m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:08 UTC 2015 HIGBLAST +06m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:18 UTC 2015 HIGBLAST +06m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:28 UTC 2015 HIGBLAST +06m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:38 UTC 2015 HIGBLAST +06m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:48 UTC 2015 HIGBLAST +06m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:42:58 UTC 2015 HIGBLAST +06m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:08 UTC 2015 HIGBLAST +07m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:18 UTC 2015 HIGBLAST +07m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:28 UTC 2015 HIGBLAST +07m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:38 UTC 2015 HIGBLAST +07m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:48 UTC 2015 HIGBLAST +07m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:43:58 UTC 2015 HIGBLAST +07m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:08 UTC 2015 HIGBLAST +08m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:18 UTC 2015 HIGBLAST +08m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:28 UTC 2015 HIGBLAST +08m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:38 UTC 2015 HIGBLAST +08m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:48 UTC 2015 HIGBLAST +08m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:44:58 UTC 2015 HIGBLAST +08m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:08 UTC 2015 HIGBLAST +09m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:18 UTC 2015 HIGBLAST +09m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:28 UTC 2015 HIGBLAST +09m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:38 UTC 2015 HIGBLAST +09m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:48 UTC 2015 HIGBLAST +09m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:45:58 UTC 2015 HIGBLAST +09m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:08 UTC 2015 HIGBLAST +10m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:18 UTC 2015 HIGBLAST +10m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:28 UTC 2015 HIGBLAST +10m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:38 UTC 2015 HIGBLAST +10m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:48 UTC 2015 HIGBLAST +10m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:46:58 UTC 2015 HIGBLAST +10m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:08 UTC 2015 HIGBLAST +11m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:18 UTC 2015 HIGBLAST +11m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:28 UTC 2015 HIGBLAST +11m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:38 UTC 2015 HIGBLAST +11m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:48 UTC 2015 HIGBLAST +11m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:47:58 UTC 2015 HIGBLAST +11m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:08 UTC 2015 HIGBLAST +12m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:18 UTC 2015 HIGBLAST +12m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:28 UTC 2015 HIGBLAST +12m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:38 UTC 2015 HIGBLAST +12m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:48 UTC 2015 HIGBLAST +12m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:48:58 UTC 2015 HIGBLAST +12m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:08 UTC 2015 HIGBLAST +13m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:18 UTC 2015 HIGBLAST +13m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:28 UTC 2015 HIGBLAST +13m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:38 UTC 2015 HIGBLAST +13m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:48 UTC 2015 HIGBLAST +13m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:49:58 UTC 2015 HIGBLAST +13m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:08 UTC 2015 HIGBLAST +14m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:18 UTC 2015 HIGBLAST +14m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:28 UTC 2015 HIGBLAST +14m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:38 UTC 2015 HIGBLAST +14m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:48 UTC 2015 HIGBLAST +14m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:50:58 UTC 2015 HIGBLAST +14m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:51:08 UTC 2015 HIGBLAST +15m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:51:18 UTC 2015 HIGBLAST +15m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:51:28 UTC 2015 HIGBLAST +15m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:51:38 UTC 2015 HIGBLAST +15m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.


[Thu Sep 17 18:51:48 UTC 2015 HIGBLAST +15m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:51:58 UTC 2015 HIGBLAST +15m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:08 UTC 2015 HIGBLAST +16m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:18 UTC 2015 HIGBLAST +16m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:28 UTC 2015 HIGBLAST +16m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:38 UTC 2015 HIGBLAST +16m31s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:48 UTC 2015 HIGBLAST +16m41s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:52:58 UTC 2015 HIGBLAST +16m51s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:53:08 UTC 2015 HIGBLAST +17m01s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:53:18 UTC 2015 HIGBLAST +17m11s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.
[Thu Sep 17 18:53:28 UTC 2015 HIGBLAST +17m21s] Loaded 6911 reads. Processed 6725 reads, of them 99.94% mapped. Among mapped reads 100.0% passed quality filter and 100.0% passed all filters.

The process then hangs after repeating that message for a while. If I kill the process, the file is output at the end, but strangely is missing the cdr3aa column.

Unmapped reads output

Add a corresponding option in CLI, output reads for which clonotypes failed to extract
Also consider providing read details as currently the script parses FASTQ to a set of non-redundant sequences and does not retain such info

Investigate spurious mappings like this one

AAGTAGTCCTTGACCAGGCACGTGATGGTGGCCGACTCCCGCAGGTTCAGCTGCTCCC
GGGCTGGTGGCAGCAAGTAGACATCGGGCCTGTGCAGGGCCACCCCCTTGGGCCGGGA
GATGGTCTGCTTCAGTGGCGAGGGCAGGTCTGTGTGGGTCACGGTGCACGTGAACCTC
TCCCCGGAATTCCAGTCATCCTCGCAGATGCTGGCCTCACCCACGGCGCTGAAAGTGG
CATTGGGGTGGCTCTCGGAGATGTTGGTGTGGGTTTTCACAGCTTCGCCATTCTTGGC
GTTGTCTCTGGAGATGGTGAATCGGCCCTTCACTGAGTCTGCGTAGTATATGTAACTA
GTACTACTAATGGATGAGACCCACTCCAGAGACAACGCCAAGAACTCACTGTATCTGC
AAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGCGATCGGAA
CGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGGAGTGCATCC
GCCCCAACCCTTTTCCCCCTCTCTGCGTTGATACCACTG

Segment alleles

Consider implementing an option to map against full V/J allele database

Include non-functional alleles

Right now alleles with no Cys residue are dropped.
These can still be retained, and marked as "no cdr3", as IgBlast allows such alignments (just make sure that no procedures that involve CDR3 mapping are performed).
This one is critical for oncohematology