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Old 08-13-2012, 06:09 PM   #21
nilshomer
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Quote:
Originally Posted by ymc View Post
Dead project now? Are there other alternatives that work on the whole genome?
It's not a dead project, feel free to post questions and bug reports etc.
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Old 08-14-2012, 04:39 AM   #22
adaptivegenome
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Quote:
Originally Posted by ymc View Post
Dead project now? Are there other alternatives that work on the whole genome?
I have used it and it is fast. I have sometimes had trouble with files in the 100GB range but generally it works fine.

We have also parallelized the GATK implementation of LR if you are interested. I am not sure which is better at realigning. I do remember comparing SRMA and GATK LR and there are differences but it was not clear to me if one was consistently better than the other. I suspect that Nils would be a better source for info on that.
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Old 08-16-2012, 05:11 AM   #23
ymc
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Tried several bams with 0.1.16 but all I got was this:

at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
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Old 08-16-2012, 06:53 AM   #24
nilshomer
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Quote:
Originally Posted by ymc View Post
Tried several bams with 0.1.16 but all I got was this:

at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
Could you post the full error message?
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Old 08-17-2012, 12:00 AM   #25
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I have been interested in this tool for some time but never got it working:
Input is a sorted bam.

java -Xmx16g -jar srma-0.1.15.jar I=491_full_s.bam O=srma_491.bam R=../NC_002516.fna
[Fri Aug 17 10:00:54 CEST 2012] srma.SRMA INPUT=[491_full_s.bam] OUTPUT=[srma_491.bam] REFERENCE=../NC_002516.fna OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/colin2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
java.util.NoSuchElementException
at java.util.Scanner.nextLine(Scanner.java:1503)
at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:131)
at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
at srma.SRMA.doWork(SRMA.java:131)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at srma.SRMA.main(SRMA.java:98)
Please report bugs to srma-help@lists.sourceforge.net


The fasta index file looks like this:

more ../NC_002516.fna.fai
NC_002516.2 6264404 58 70 71

Cheers for any help.
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Old 08-18-2012, 10:05 AM   #26
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There are thousands of lines of these error messages. If I copy the stderr output, it will be too many lines. You can replicate my problem by downloading the pair-ended reads from

ftp://ftp.1000genomes.ebi.ac.uk/vol1...sequence_read/

and then align them using bwa. I got the same bug with SRR098401_*.filt.fastq.gz and SRR035330_*.filt.fastq.gz
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Old 08-18-2012, 12:39 PM   #27
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Quote:
Originally Posted by colindaven View Post
I have been interested in this tool for some time but never got it working:
Input is a sorted bam.

java -Xmx16g -jar srma-0.1.15.jar I=491_full_s.bam O=srma_491.bam R=../NC_002516.fna
[Fri Aug 17 10:00:54 CEST 2012] srma.SRMA INPUT=[491_full_s.bam] OUTPUT=[srma_491.bam] REFERENCE=../NC_002516.fna OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/colin2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
java.util.NoSuchElementException
at java.util.Scanner.nextLine(Scanner.java:1503)
at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:131)
at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
at srma.SRMA.doWork(SRMA.java:131)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at srma.SRMA.main(SRMA.java:98)
Please report bugs to srma-help@lists.sourceforge.net


The fasta index file looks like this:

more ../NC_002516.fna.fai
NC_002516.2 6264404 58 70 71

Cheers for any help.
It looks like your FASTA index is broken. Can you try rebuilding?

Quote:
Originally Posted by ymc View Post
There are thousands of lines of these error messages. If I copy the stderr output, it will be too many lines. You can replicate my problem by downloading the pair-ended reads from

ftp://ftp.1000genomes.ebi.ac.uk/vol1...sequence_read/

and then align them using bwa. I got the same bug with SRR098401_*.filt.fastq.gz and SRR035330_*.filt.fastq.gz
I am sorry, please try reducing your read set or the like to a manageable test case. Otherwise, I charge $5KUSD/hour
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Old 04-17-2014, 08:29 AM   #28
madonjoe
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Default Empty VCF file

I tried to use SRMA to realign my reads and did a variant calling. However, after SRMA, which ran fine, I got an empty vcf file. Anything I can do to fix this problem?
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