I'm trying to get csv files from snpEff and the option -csvStats and got stuck.

I tried the code below and only got the vcf file with no contents.

How to use -csvStats option properly?

I would really appreciate your help.

snpEff -Xmx4g -csvStats -v hg19 08_FILTER/NA12878.Filtered.Variants.vcf > test.ann.vcf



00:00:00    SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00    Command: 'ann'
00:00:00    Reading configuration file 'snpEff.config'. Genome: '08_FILTER/NA12878.Filtered.Variants.vcf'
00:00:00    Reading config file: /home/ubuntu/01_NA12878/snpEff.config
00:00:00    Reading config file: /home/ubuntu/miniconda2/share/snpeff-4.3.1t-2/snpEff.config
java.lang.RuntimeException: Property: '08_FILTER/NA12878.Filtered.Variants.vcf.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:106)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:00    Logging

00:00:01    Done.

snpEff -Xmx4g -v hg19 -csvStats 08_FILTER/NA12878.Filtered.Variants.vcf > tes2.ann.vcf



00:00:25    Genome stats :
#-----------------------------------------------
# Genome name                : 'Homo_sapiens (USCS)'
# Genome version             : 'hg19'
# Genome ID                  : 'hg19[0]'
# Has protein coding info    : true
# Has Tr. Support Level info : true
# Genes                      : 29583
# Protein coding genes       : 20797
#-----------------------------------------------
# Transcripts                : 60834
# Avg. transcripts per gene  : 2.06
# TSL transcripts            : 0
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :      0 ( 0.00% )
#              DNA sequences :  52386 ( 86.11% )
#-----------------------------------------------
# Protein coding transcripts : 46522
#              Length errors :     93 ( 0.20% )
#  STOP codons in CDS errors :     78 ( 0.17% )
#         START codon errors :    117 ( 0.25% )
#        STOP codon warnings :     19 ( 0.04% )
#              UTR sequences :  45868 ( 75.40% )
#               Total Errors :    256 ( 0.55% )
#-----------------------------------------------
# Cds                        : 460256
# Exons                      : 570329
# Exons with sequence        : 570329
# Exons without sequence     : 0
# Avg. exons per transcript  : 9.38
#-----------------------------------------------
# Number of chromosomes      : 94
# Chromosomes                : Format 'chromo_name size codon_table'
#       '1' 249250621   Standard
#       '2' 243199373   Standard
#       '3' 198022430   Standard
#       '4' 191154276   Standard
#       '5' 180915260   Standard
#       '6' 171115067   Standard
#       '7' 159138663   Standard
#       'X' 155270560   Standard
#       '8' 146364022   Standard
#       '9' 141213431   Standard
#       '10'    135534747   Standard
#       '11'    135006516   Standard
#       '12'    133851895   Standard
#       '13'    115169878   Standard
#       '14'    107349540   Standard
#       '15'    102531392   Standard
#       '16'    90354753    Standard
#       '17'    81195210    Standard
#       '18'    78077248    Standard
#       '20'    63025520    Standard
#       'Y' 59373566    Standard
#       '19'    59128983    Standard
#       '22'    51304566    Standard
#       '21'    48129895    Standard
#       '6_ssto_hap7'   4928567 Standard
#       '6_mcf_hap5'    4833398 Standard
#       '6_cox_hap2'    4795371 Standard
#       '6_mann_hap4'   4683263 Standard
#       '6_apd_hap1'    4622290 Standard
#       '6_qbl_hap6'    4611984 Standard
#       '6_dbb_hap3'    4610396 Standard
#       '17_ctg5_hap1'  1680828 Standard
#       '4_ctg9_hap1'   590426  Standard
#       '1_gl000192_random' 547496  Standard
#       'Un_gl000225'   211173  Standard
#       '4_gl000194_random' 191469  Standard
#       '4_gl000193_random' 189789  Standard
#       '9_gl000200_random' 187035  Standard
#       'Un_gl000222'   186861  Standard
#       'Un_gl000212'   186858  Standard
#       '7_gl000195_random' 182896  Standard
#       'Un_gl000223'   180455  Standard
#       'Un_gl000224'   179693  Standard
#       'Un_gl000219'   179198  Standard
#       '17_gl000205_random'    174588  Standard
#       'Un_gl000215'   172545  Standard
#       'Un_gl000216'   172294  Standard
#       'Un_gl000217'   172149  Standard
#       '9_gl000199_random' 169874  Standard
#       'Un_gl000211'   166566  Standard
#       'Un_gl000213'   164239  Standard
#       'Un_gl000220'   161802  Standard
#       'Un_gl000218'   161147  Standard
#       '19_gl000209_random'    159169  Standard
#       'Un_gl000221'   155397  Standard
#       'Un_gl000214'   137718  Standard
#       'Un_gl000228'   129120  Standard
#       'Un_gl000227'   128374  Standard
#       '1_gl000191_random' 106433  Standard
#       '19_gl000208_random'    92689   Standard
#       '9_gl000198_random' 90085   Standard
#       '17_gl000204_random'    81310   Standard
#       'Un_gl000233'   45941   Standard
#       'Un_gl000237'   45867   Standard
#       'Un_gl000230'   43691   Standard
#       'Un_gl000242'   43523   Standard
#       'Un_gl000243'   43341   Standard
#       'Un_gl000241'   42152   Standard
#       'Un_gl000236'   41934   Standard
#       'Un_gl000240'   41933   Standard
#       '17_gl000206_random'    41001   Standard
#       'Un_gl000232'   40652   Standard
#       'Un_gl000234'   40531   Standard
#       '11_gl000202_random'    40103   Standard
#       'Un_gl000238'   39939   Standard
#       'Un_gl000244'   39929   Standard
#       'Un_gl000248'   39786   Standard
#       '8_gl000196_random' 38914   Standard
#       'Un_gl000249'   38502   Standard
#       'Un_gl000246'   38154   Standard
#       '17_gl000203_random'    37498   Standard
#       '8_gl000197_random' 37175   Standard
#       'Un_gl000245'   36651   Standard
#       'Un_gl000247'   36422   Standard
#       '9_gl000201_random' 36148   Standard
#       'Un_gl000235'   34474   Standard
#       'Un_gl000239'   33824   Standard
#       '21_gl000210_random'    27682   Standard
#       'Un_gl000231'   27386   Standard
#       'Un_gl000229'   19913   Standard
#       'M' 16571   Vertebrate_Mitochondrial
#       'Un_gl000226'   15008   Standard
#       '18_gl000207_random'    4262    Standard
#       'MT'    1   Vertebrate_Mitochondrial
#-----------------------------------------------

00:00:27    Predicting variants