Hello, I am getting these errors when running soapsnp (infact I am running crossbow and it is in turn running soapsnp) . Any help would be appreciated.
Code:
* reporter:counter:SOAPsnp,Occurrences of quality value [30:40) in wrapper,543
* reporter:counter:SOAPsnp,Occurrences of quality value [20:30) in wrapper,801
* reporter:counter:SOAPsnp,Occurrences of quality value [10:20) in wrapper,1311
* reporter:counter:SOAPsnp,Occurrences of quality value [40:50) in wrapper,4704
* reporter:counter:SOAPsnp,Occurrences of quality value [0:10) in wrapper,2678
* reporter:counter:SOAPsnp,Occurrences of quality value [30:40) in wrapper,568
* reporter:counter:SOAPsnp,Occurrences of quality value [20:30) in wrapper,747
* reporter:counter:SOAPsnp,Occurrences of quality value [10:20) in wrapper,1326
* reporter:counter:SOAPsnp,Occurrences of quality value [40:50) in wrapper,4748
* reporter:counter:SOAPsnp,Occurrences of quality value [0:10) in wrapper,2607
* reporter:counter:SOAPsnp,Occurrences of quality value [30:40) in wrapper,549
* reporter:counter:SOAPsnp,Occurrences of quality value [20:30) in wrapper,778
* reporter:counter:SOAPsnp,Occurrences of quality value [10:20) in wrapper,1347
* reporter:counter:SOAPsnp,Occurrences of quality value [40:50) in wrapper,4565
* reporter:counter:SOAPsnp,Occurrences of quality value [0:10) in wrapper,2762
* reporter:counter:SOAPsnp,Occurrences of quality value [30:40) in wrapper,594
* reporter:counter:SOAPsnp,Occurrences of quality value [20:30) in wrapper,740
* Read the last line of input
* reporter:counter:SOAPsnp wrapper,Ranges processed,1
* reporter:counter:SOAPsnp wrapper,Alignments processed,761653
* Soapsnp.pl: Genotyping chromosome 0 3000000-4000000 using 761653 alignments: Wed Feb 22 17:33:29 IST 2012
* Soapsnp.pl: chromosome 0 is haploid; using args "-r 0.0001 -m"
* Soapsnp.pl: head -4 .tmp.1000000.0003:
* 0 0003 002999964 + GATGTTTAAGGCGCGGTCAGCATTTCCAGATCGCTA IAIAIIIIIGIII9'I<./7&/DII".+(%'#&"%' 0 33:A>C 0 r
* 0 0003 002999965 + ATGTTTAAGGCGCGGTCAGCATTTCCAGATCGTTCC IIIIIIIIIIIIIIIID1IE6III)0"+'/*%"("% 0 32:A>T,34:A>C,35:A>C 0 r
* 0 0003 002999967 - GTGGAAGGCGCGGTAAGCATTTCCAGATCGATAAGC &)"#&%&&"#'&-6%'*(6I-79=IC@IIIIIIIII 0 21:C>A,32:T>G,33:T>G 0 r
* 0 0003 002999968 - TAAAAGGCGCGGTCATCATTTCCAGATCGATAAGCC "#$"+""&#+%#($*#%+,*,%(;-00.F?3II:I7 0 20:G>T,33:T>A,34:T>A 0 r
* Soapsnp.pl: tail -4 .tmp.1000000.0003:
* 0 0003 003999994 + CTGGATCTTCTTTGCCCAGCGCCGCCGGACCGTTTT IIIIIIIIIIIIIIIIII4:I8I-<%A"#$$-%)'$ 0 25:A>C,28:G>A,29:A>C,32:A>T,35:G>T 0 r
* 0 0003 003999996 + GGATCTTCTTTGCCCAGCGCCGCAGGTTCGGTTTCG IICIIIIIIIIAIII2II=G<II+10""))",$%"$ 0 26:G>T,27:A>T,30:A>G,33:G>T,34:A>C 0 r
* 0 0003 003999999 + TCTTCTTTGCCCAGCGCCGCCGGCACGATTGAGAGT @@II8IIHCI266I&46*3/"/#"('*#)#$"""&% 0 20:A>C,23:G>C,34:A>G,35:G>T 0 r
* 0 0003 003999999 - TGAGCTATGACCAGCGCCGCAGGAACGATTGAGAAG """#&"#""&3$-&=%0I=II>IIIIAI+9IIIIII 0 12:G>A,26:C>A,29:T>A,32:T>G,33:T>A,34:C>G 0 r
* reporter:counter:SOAPsnp wrapper,SNP files missing,1
* Soapsnp.pl: Warning: /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/snps/0.snps doesn't exist
* Soapsnp.pl: ls -l /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/snps
* Soapsnp.pl: total 0
* Soapsnp.pl: Warning: neither /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/snps/chr0.snps nor /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/snps/0.snps exist; not using known SNPs
* Soapsnp.pl: ls -al /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/snps
* Soapsnp.pl: total 8
* drwxr-xr-x 2 xyzuser hadoop 4096 2012-02-22 09:36 .
* drwxr-xr-x 6 xyzuser hadoop 4096 2012-02-22 09:36 ..
* Soapsnp.pl: /home/xyzuser//cbexec/bin/linux32/soapsnp -i .tmp.1000000.0003 -d /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/sequences/chr0.fa -o .tmp.snps -z '!' -L 36 -c -H -T .range_3000000_4000000 -r 0.0001 -m -2 -u -n -q >.soapsnp.14632.stdout 2>.soapsnp.14632.stderr
* Soapsnp.pl: soapsnp returned 33792
* Soapsnp.pl: command: /home/xyzuser//cbexec/bin/linux32/soapsnp -i .tmp.1000000.0003 -d /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/sequences/chr0.fa -o .tmp.snps -z '!' -L 36 -c -H -T .range_3000000_4000000 -r 0.0001 -m -2 -u -n -q >.soapsnp.14632.stdout 2>.soapsnp.14632.stderr
* Soapsnp.pl: stdout from soapsnp:
* Soapsnp.pl: stderr from soapsnp:
* -i is set to .tmp.1000000.0003
* -d is set to /home/xyzuser/bio/crossbow/crossbow-1.1.2/crossref/e_coli/sequences/chr0.fa
* -o is set to .tmp.snps
* Standard Fastq System Set
* -L is set to 36
* -c is set
* -T is set to .range_3000000_4000000
* -r is set to 0.0001
* -m is set
* -2 is set
* -u is set
* -n is set
* -q is set
* Read 5498450 from 78551 lines of input FASTA sequence 17:33:29
* Finished loading and binarizing chromosome 17:33:29
* Finished parsing 0 known SNPs 17:33:29
* Reading Chromosome and dbSNP information Done.
* Read target region done.
* Training correction matrix in Crossbow format17:33:30
* Correction Matrix Done 17:33:38
* Illegal instruction
* Soapsnp.pl: range: 0 3000000 4000000
* Soapsnp.pl: head -4 .tmp.snps:
* Soapsnp.pl: tail -4 .tmp.snps:
* Dying following soapsnp returning non-zero 33792 at /home/xyzuser//cbexec/Soapsnp.pl line 372.
******
Fatal error 1.1.2:R330: Aborting because child with PID 14405 exited abnormally
When requesting support, please include the full output printed here.
If a child process was the cause of the error, the output should
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be asked to provide additional files as well.
Non-zero exitlevel from SNP calling stage