Hi,
Does anyone have a recommended read-trimming software that works with color-space data?
Also, I'm not trying to-repost but I'm getting some odd-errors and the help-email list for SamTools seems dead. What is the source of this error:
INFO 2010-10-29 09:39:34 MarkDuplicates Read 46000000 records. Tracking 687328 as yet unmatched pairs. 46728 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:39:45 MarkDuplicates Read 47000000 records. Tracking 686480 as yet unmatched pairs. 32624 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:40:08 MarkDuplicates Read 48000000 records. Tracking 684660 as yet unmatched pairs. 17477 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:40:18 MarkDuplicates Read 49000000 records. Tracking 682311 as yet unmatched pairs. 479 records in RAM. Last sequence index: 9
[Fri Oct 29 09:40:37 CDT 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=772931584
Exception in thread "main" net.sf.picard.PicardException: Exception writing ReadEnds to file.
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:74)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:32)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:269)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:260)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at java.io.DataOutputStream.flush(DataOutputStream.java:106)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:71)
... 7 more
I can't seem to find any documentation on it and nobody answered my last post.
Finally, I've been reading on some previous seq-answers posts and I wanted to see if anyone can clarify that samtools removes duplicates based on start/stop alone and doesn't consider identical sequences. Are you sure?
Does anyone have a recommended read-trimming software that works with color-space data?
Also, I'm not trying to-repost but I'm getting some odd-errors and the help-email list for SamTools seems dead. What is the source of this error:
INFO 2010-10-29 09:39:34 MarkDuplicates Read 46000000 records. Tracking 687328 as yet unmatched pairs. 46728 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:39:45 MarkDuplicates Read 47000000 records. Tracking 686480 as yet unmatched pairs. 32624 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:40:08 MarkDuplicates Read 48000000 records. Tracking 684660 as yet unmatched pairs. 17477 records in RAM. Last sequence index: 9
INFO 2010-10-29 09:40:18 MarkDuplicates Read 49000000 records. Tracking 682311 as yet unmatched pairs. 479 records in RAM. Last sequence index: 9
[Fri Oct 29 09:40:37 CDT 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=772931584
Exception in thread "main" net.sf.picard.PicardException: Exception writing ReadEnds to file.
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:74)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:32)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:269)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:260)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at java.io.DataOutputStream.flush(DataOutputStream.java:106)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:71)
... 7 more
I can't seem to find any documentation on it and nobody answered my last post.
Finally, I've been reading on some previous seq-answers posts and I wanted to see if anyone can clarify that samtools removes duplicates based on start/stop alone and doesn't consider identical sequences. Are you sure?
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