Hi, I downloaded SCNVSim a month ago, and was planning on using SCNVSim to simulate some CNV datasets. It seems there are some issues:
1) below is the command line I typed:
java -jar -v chrom_length -n hg19.fasta -o out_directory
According to the manual, if the output directory does not exist when the command is executed, then it will be created. However, I don't think the 'out_directory' was created when I executed the command line, instead, it throws an error message saying the directory can not be found.
2) Even if I manually create the output directory before executing the command line, it still keeps throwing this error message;
INFO: Simulating snv and indels for chr1
Exception in thread "main" net.sf.picard.PicardException: Unable to find entry for contig: 1
at net.sf.picard.reference.FastaSequenceIndex.getIndexEntry(FastaSequenceIndex.java:166)
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181)
at org.rpci.snvindel.util.SequenceRetriever.getLocalFragment(SequenceRetriever.java:42)
at org.rpci.snvindel.SimulateSNV.generateSingleSNV(SimulateSNV.java:118)
at org.rpci.snvindel.SnvIndelSimulator.generateSNPIndels(SnvIndelSimulator.java:177)
at org.rpci.snvindel.SnvIndelSimulator.main(SnvIndelSimulator.java:293)
What is this error about??
Are these the bugs that the author is working on? Do you have a timeline for that? I need to get some results by the end of this week.
Thank you,
JC
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Thank you for reporting bugs to us on SCNVSIM.
The answer to your first question is that if you specify -o, the directory you specified should be existing. If you don't specify -o option, a temparary output directory would be created. That's a good point, I should check if the output directory given by users exists and create that one if it can't be found. But this time I didn't work on this.
About the second question, the error was generated because of the chromosome ids in reference fasta file and the chromosome length file are not consistant. sometimes there are "chr"s, but sometimes not. I have solved this kind of problem. I just uploaded the new version of this tool. You can try it and if you still have this problem, please let me know.
Thanks again.
Maochun
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The SCNVSim project folder was removed because the project owner is working on some bugs.
Hi, I downloaded SCNVSim a month ago, and was planning on using SCNVSim to simulate some CNV datasets. It seems there are some issues:
1) below is the command line I typed:
java -jar -v chrom_length -n hg19.fasta -o out_directory
According to the manual, if the output directory does not exist when the command is executed, then it will be created. However, I don't think the 'out_directory' was created when I executed the command line, instead, it throws an error message saying the directory can not be found.
2) Even if I manually create the output directory before executing the command line, it still keeps throwing this error message;
INFO: Simulating snv and indels for chr1
Exception in thread "main" net.sf.picard.PicardException: Unable to find entry for contig: 1
at net.sf.picard.reference.FastaSequenceIndex.getIndexEntry(FastaSequenceIndex.java:166)
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181)
at org.rpci.snvindel.util.SequenceRetriever.getLocalFragment(SequenceRetriever.java:42)
at org.rpci.snvindel.SimulateSNV.generateSingleSNV(SimulateSNV.java:118)
at org.rpci.snvindel.SnvIndelSimulator.generateSNPIndels(SnvIndelSimulator.java:177)
at org.rpci.snvindel.SnvIndelSimulator.main(SnvIndelSimulator.java:293)
What is this error about??
Are these the bugs that the author is working on? Do you have a timeline for that? I need to get some results by the end of this week.
Thank you,
JC
Hi, Jackie,
Thank you for reporting bugs to us on SCNVSIM.
The answer to your first question is that if you specify -o, the directory you specified should be existing. If you don't specify -o option, a temparary output directory would be created. That's a good point, I should check if the output directory given by users exists and create that one if it can't be found. But this time I didn't work on this.
About the second question, the error was generated because of the chromosome ids in reference fasta file and the chromosome length file are not consistant. sometimes there are "chr"s, but sometimes not. I have solved this kind of problem. I just uploaded the new version of this tool. You can try it and if you still have this problem, please let me know.
Thanks again.
Maochun