Entering edit mode
8.1 years ago
waqasnayab
▴
250
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.
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.
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
Hello, don't post comment here, this is place for answer. Have you try to adjust
-Xmxvalue to bigger? I think you can start a new post, this post is too old,snpEffmay changed a lot, your problem may not the same with this.As MatthewP says, do not add an answer unless you're answering the top level question. I've moved your post to a comment.