Question: snpEFF job stucks without any error
0
gravatar for waqasnayab
3.7 years ago by
waqasnayab200
Pakistan
waqasnayab200 wrote:

Hi,

I am running snpEEff.

/home/sci/Desktop/usr/java/jdk1.7.0_79/bin/java -Xmx48g -Djava.io.tmpdir=java_tmp \
-XX:MaxPermSize=512m -XX:-UseGCOverheadLimit \
-jar /home/sci/Desktop/snpEff/snpEff.jar hg19 -v \
-stats out_annt_144_dp10.vcf > out_annt_144_dp10_snpeff.vcf

The top command also shows that the job is running. After 5-6 minutes, the job disappeared and the verbose stops at:

[sci@pen 4_8]$ 
[sci@pen 4_8]$ /home/sci/Desktop/usr/java/jdk1.7.0_79/bin/java -Xmx48g -Djava.io.tmpdir=java_tmp 
                        -XX:MaxPermSize=512m -XX:-UseGCOverheadLimit 
                        -jar /home/sci/Desktop/snpEff/snpEff.jar hg19 -v 
                        -stats out_annt_144_dp10.vcf > out_annt_144_dp10_snpeff.vcf
00:00:00    SnpEff version SnpEff 4.2 (build 2015-12-05), by Pablo Cingolani
00:00:00    Command: 'ann'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'hg19'
00:00:00    Reading config file: /data/results/Projects/sci/4_8/snpEff.config
00:00:00    Reading config file: /home/sci/Desktop/snpEff/snpEff.config
00:00:01    done
00:00:01    Reading database for genome version 'hg19' from file 
                '/home/sci/Desktop/snpEff/./data/hg19/snpEffectPredictor.bin' (this might take a while)
00:00:21    done
00:00:21    Loading Motifs and PWMs
00:00:21        Loading interactions from : /home/sci/Desktop/snpEff/./data/hg19/interactions.bin
00:00:33        Interactions: 1513647 added, 0 skipped.
00:00:33    Building interval forest
00:00:38    done.
00:00:38    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                      : 28900
# Protein coding genes       : 20761
#-----------------------------------------------
# Transcripts                : 54668
# Avg. transcripts per gene  : 1.89
# TSL transcripts            : 0
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :  36640 ( 86.72% )
#              DNA sequences :  46933 ( 85.85% )
#-----------------------------------------------
# Protein coding transcripts : 42252
#              Length errors :     90 ( 0.21% )
#  STOP codons in CDS errors :     83 ( 0.20% )
#         START codon errors :    121 ( 0.29% )
#        STOP codon warnings :     19 ( 0.04% )
#              UTR sequences :  41579 ( 76.06% )
#               Total Errors :    254 ( 0.60% )
#-----------------------------------------------
# Cds                        : 419731
# Exons                      : 510146
# Exons with sequence        : 510146
# Exons without sequence     : 0
# Avg. exons per transcript  : 9.33
#-----------------------------------------------
# Number of chromosomes      : 93
# 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
#-----------------------------------------------

00:00:49    Predicting variants

I did not see any error. No output is formed. Is this a software issue or java or input problem?

Thanks,

Waqas.

snp software error • 1.4k views
ADD COMMENTlink modified 4 months ago by amandaspadovan0 • written 3.7 years ago by waqasnayab200

Please do not use scary big fonts. Machine generated lines of text (such as contents of output or error streams) are best placed in code blocks. I will now correct this for you.

ADD REPLYlink written 3.7 years ago by RamRS24k

Did you ever find a solution to this problem? I am having the same issue now. I have run snpEff heaps in the last 12 months and never encountered this problem before. Best wishes, Amanda

ADD REPLYlink written 4 months ago by amandaspadovan0

Hello, don't post comment here, this is place for answer. Have you try to adjust -Xmx value to bigger? I think you can start a new post, this post is too old, snpEff may changed a lot, your problem may not the same with this.

ADD REPLYlink written 4 months ago by MatthewP290

As MatthewP says, do not add an answer unless you're answering the top level question. I've moved your post to a comment.

ADD REPLYlink written 4 months ago by RamRS24k
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