vBestIdentityPercent value NaN

[kwuiee]

Hi,

I am using MIXCR for some SHM calculations. One of my samples shows a clone with vBestIdentityPercent value NaN. Wondering how this happened. Is the value expected or not?

cloneId	cloneCount	cloneFraction	targetSequences	targetQualities	allVHitsWithScore	allDHitsWithScore	allJHitsWithScore	allCHitsWithScore	allVAlignments	allDAlignments	allJAlignments	allCAlignments	nSeqFR1	minQualFR1	nSeqCDR1	minQualCDR1	nSeqFR2	minQualFR2	nSeqCDR2	minQualCDR2	nSeqFR3	minQualFR3	nSeqCDR3	minQualCDR3	nSeqFR4	minQualFR4	aaSeqFR1	aaSeqCDR1	aaSeqFR2	aaSeqCDR2	aaSeqFR3	aaSeqCDR3	aaSeqFR4	refPoints	vBestIdentityPercent	vIdentityPercents
3	209884	0.294703	CCCTGAGACTCTCCTGTGCAG,GGCGGATCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGATTTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAATGATTATATCAAATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGACCGGGTGGGGACACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAACGTCAGCTG	[[[[[[[[[[[[[[[[[[[[[,0.-3+++40212<;798<67:8?8@@>B=C::;@=:;:E>:=8;>?=;:8?:>=;=:?>=<::@C>:;96655<@3:6,2*4<++9,26/3:;9;-:27693:D?::9=<><7;,,,+113,;=88<:;3@<>>968<@;=;>:<:>::><<99<09<@<+?=:;9;<=@%B<B<==9<A==9<<:9C<7;:>>::;8AA>@@><;;=9<@;B<B;?1??=6C<=<<@aa>9;6?A==>;------------------------------------A?@@>=>C5;@<(%?9=5>:):4>));.).:;---3-,4;/117	IGHV3-11*00(1447.5)	IGHD2-2100(31),IGHD6-1900(30),IGHD7-27*00(30)	IGHJ6*00(339.2)	IGHG100(0),IGHG200(0),IGHG300(0),IGHG400(0),IGHGP*00(0)	291|291|570|21|21||0.0,296|546|570|0|247|SA298CSG301ASG357TSC358TSG411ASA413GSG414ADG416DG417DG420SC423TST426A|2118.0	,38|47|84|250|259|ST43G|31.0;,19|25|63|247|253||30.0;,16|22|33|252|258||30.0	,40|83|83|264|307|SA55C|401.0	,;,;,;,;,			GGATTCACCTTCAGTGACTACTAC	23	ATGATTTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATAC	9	ATTAGTAATGATTATATCAAA	10	TACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTAC	4	TGTGCGACCGGGTGGGGACACGGTATGGACGTCTGG	12	GGCCAAGGGACCACGGTCACCGTCTCCTCAG	4		GFTFSDYY	MIWIRQAPGKGLEWVSY	ISNDYIK	YYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYY	CATGWGHGMDVW	GQGTTVTVSS_	:::::::::::::::::::::,:::::33:57:108:129:240:-4:247:250:-10:-9:259:264:-20:276:307::	NaN	NaN

best

[mizraelson]

Hi, can you share the exact commands you used starting from analyze?

[kwuiee]

Hi, can you share the exact commands you used starting from analyze?

The command gave NaN shows below

java -Xmx15g -Xms15g  -Djava.io.tmpdir=/tmp -jar /bioapp/mixcr.jar align \
    -t 12 --species hsa -p kaligner2 -OallowPartialAlignments=false -OvParameters.geneFeatureToAlign=VGeneWithP  \
    --report sample.alignment.log \
    sampe_1.clean.fq.gz \
    sample_2.clean.fq.gz \
    sample.alignment.vdjca -f 

java -Xmx100g -Xms30g  -Djava.io.tmpdir=/tmp -jar /bioapp/mixcr.jar assemble \
    --write-alignments -f -t 12 \
    sample.alignment.vdjca \
    sample.alignment.clna

java -Xmx100g -Xms30g  -Djava.io.tmpdir=/tmp -jar /bioapp/mixcr.jar assembleContigs \
    -f -t 12 \
    sample.alignment.clna \
    sample.full.alignment.clns

java -Xmx100g -Xms30g  -Djava.io.tmpdir=/tmp -jar /bioapp/mixcr.jar exportClones \
    --chains IGH -f --preset full -vBestIdentityPercent -vIdentityPercents \
    sample.full.alignment.clns \
    sample_heavyChain_full.xls

By the way, my MIXCR version is 3.0.13, I think.

[mizraelson]

Can you please try the latest version and confirm the issue is still present? also what type of data is it, bulk RNAseq?

[kwuiee]

It is bulk DNAseq data. It is weird to give a not NaN value when using almost half reads from fastq. The latter case targetSequence CGGCGGATCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGATTTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAATGATTATATCAAATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGACCGGGTGGGGACACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAACGTCAGCTG differs a CCCTGAGACTCTCCTGTGCAG,. I will try to use the latest version.

[mizraelson]

with the latest version you can use the following command:

mixcr analyze exome-seq \
    --species hsa \
    --append-export-clones-field -vIdentityPercents \
    --append-export-clones-field -vBestIdentityPercent \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result

[kwuiee]

with the latest version you can use the following command:

mixcr analyze exome-seq \
    --species hsa \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result

Thanks a lot