TotalReads count not set about mixcr HOT 10 CLOSED

#!/bin/bash
#
#$ -cwd
module load java/8
module load mixcr/4.1.2
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar align -p rnaseq-cdr3 --verbose -s hsa -OallowPartialAlignments=true -OvParameters.geneFeatureToAlign=VGeneWithP -r /cluster/path/to/mixcr4/log/LOG_ALIGN_file.txt /cluster/path/to/data/file_R1.fastq /cluster/path/to/data/file_R2.fastq /cluster/path/to/mixcr4/alignments/alignments_file.vdjca
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar assemblePartial /cluster/path/to/mixcr4/alignments/alignments_file.vdjca /cluster/path/to/mixcr4/assemble/rescue1_file.vdjca
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar assemblePartial /cluster/path/to/mixcr4/assemble/rescue1_file.vdjca /cluster/path/to/mixcr4/assemble/rescue2_file.vdjca
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar extend /cluster/path/to/mixcr4/assemble/rescue2_file.vdjca /cluster/path/to/mixcr4/assemble/extended_file.vdjca
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar assemble -r /cluster/path/to/mixcr4/log/LOG_ASSEMBLE_file.txt /cluster/path/to/mixcr4/assemble/extended_file.vdjca /cluster/path/to/mixcr4/assemble/file.clns
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar exportClones --chains TRA /cluster/path/to/mixcr4/assemble/file.clns /cluster/path/to/mixcr4/clones/CLONES_TRAfile.tsv
java -jar /cluster/path/to/mixcr/4.1.2/mixcr.jar exportClones --chains TRB /cluster/path/to/mixcr4/assemble/file.clns /cluster/path/to/mixcr4/clones/CLONES_TRBfile.tsv

Analysis time: 1128.7m
Total sequencing reads: 43390557
Successfully aligned reads: 38195684 (88.03%)
Chimeras: 5 (0%)
Paired-end alignment conflicts eliminated: 93125 (0.21%)
Alignment failed, no hits (not TCR/IG?): 1233379 (2.84%)
Alignment failed because of absence of CDR3 parts: 2129356 (4.91%)
Alignment failed because of low total score: 1832138 (4.22%)
Overlapped: 28612588 (65.94%)
Overlapped and aligned: 26198878 (60.38%)
Alignment-aided overlaps: 1127455 (4.3%)
Overlapped and not aligned: 2413710 (5.56%)
No CDR3 parts alignments, percent of successfully aligned: 44345 (0.12%)
Partial aligned reads, percent of successfully aligned: 21613444 (56.59%)
V gene chimeras: 12995 (0.03%)
J gene chimeras: 429656 (0.99%)
TRA chains: 14828702 (38.82%)
TRA non-functional: 5688903 (38.36%)
TRB chains: 4440587 (11.63%)
TRB non-functional: 570282 (12.84%)
TRD chains: 333584 (0.87%)
TRD non-functional: 59217 (17.75%)
TRG chains: 4814406 (12.6%)
TRG non-functional: 2683093 (55.73%)
TRAD chains: 13778400 (36.07%)
TRAD non-functional: 0 (0%)
Realigned with forced non-floating bound: 31810848 (73.31%)
Realigned with forced non-floating right bound in left read: 167045 (0.38%)
Realigned with forced non-floating left bound in right read: 167045 (0.38%)