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BAMToGASV #13

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
There's no BAMToGASV.jar in the /bin directory after running ./install.

Original issue reported on code.google.com by jlzhuan...@gmail.com on 13 Dec 2013 at 7:39

GoogleCodeExporter commented 8 years ago 
Thanks for your question. This suggests that the installation script did not 
work.

Do you have java, ant and gcc? 

It would also be helpful to have the output from your screen from the ./install 

(You can attach a file in your response if that would be helpful.)

Original comment by ssindi...@gmail.com on 13 Dec 2013 at 7:42

GoogleCodeExporter commented 8 years ago 
Thank you for your prompt response. 
Yes, it is a java compilation problem and I've fixed that.
However, I ran into another issue. 
When I ran ./GASVPro-HQ.sh, the output is as follows:

\n** GASVProHQ Running... **\n
====Input====
      GASVDIR...ok
      Valid .bam file: /home/zhuangj/scratch/simulated_mixture_10.sorted.bam
      No unique file Provided.
      No LR Threshold Provided
      No Min Cluster Size provided
=============\n

===================================\n\n *** Running BAMToGASV....*** 
\n\n===================================\n

===================================
Arguments are:
  BAM File = /home/zhuangj/scratch/simulated_mixture_10.sorted.bam
  Output Prefix = 2013-12-13_15:27
  Minimum Mapping Quality = 10
  Minimum Alignment Percent = 95
  Lmin/Lmax Cutoff = "PCT=99%"
  # of Reads for Calculating Lmin/Lmax, Checking Pairs, and Checking Variant Types = 500000
  Chromosome Naming File (null if none specified) = null
  Maximum Length for a Proper Pair = 10000
  Platform = "illumina"
  Write Concordant File? true
  Write SplitRead File? false
  Separate Libraries? false
  Validation Stringency: SILENT
  Prepare GASVPro Output? true
===================================

Processing Header Information...
  Genome length: 23011544
  WARNING: No library information found in the BAM.  Proceeding with -LIBRARY_SEPARATED "all" flag.
  Proceeding with the following libraries:
    "all"

Reading BAM file.  Once 500000 lines have been acquired for each library, stats 
will be calculated.
About to set up the output files

  processing BAM line 1: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 1000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 1500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 2000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 2500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 3000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 3500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 4000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 4500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 5000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 5500000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
  processing BAM line 6000000: 
    "all" has 0 lines in memory and 0 records in the first N reads.
Done reading BAM file.

  WARNING: There are fewer than 500000 for library "all". Computing statistics now...

Checking pairing info for library "all"...
WARNING: Library all has no pairing info in the first 500000 fragments.
Getting Lmin and Lmax for library "all"...
  WARNING: No paired reads found.
  Library "all" has Lmin=-2147483648 and Lmax=0 using percentile method in first 0 reads.
Checking discordant types for library all...
  WARNING: Library "all" has no inversions in first 0 reads.
  WARNING: Library "all" has no deletions in first 0 reads.
  WARNING: Library "all" has no divergents in first 0 reads.
  WARNING: Library "all" has no translocations in first 0 reads.
  WARNING: Library "all" has no insertions in first 0 reads.

Running Fixmate() to pair reads.  When this is done, re-run BAMToGASV.jar with 
the new BAM file.
Writing fixed BAM/SAM file to 2013-12-13_15:27.fixmate.bam
[Fri Dec 13 15:31:03 EST 2013] net.sf.picard.sam.FixMateInformation 
INPUT=[/home/zhuangj/scratch/simulated_mixture_10.sorted.bam] 
OUTPUT=2013-12-13_15:27.fixmate.bam    VERBOSITY=INFO QUIET=false 
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 
CREATE_INDEX=false CREATE_MD5_FILE=false
[Fri Dec 13 15:31:03 EST 2013] Executing as zhuangj@dl145-036.umasshpcc.edu on 
Linux 2.6.18-92.1.22.el5.centos.plus amd64; Java HotSpot(TM) 64-Bit Server VM 
1.6.0_16-b01; Picard version: null
INFO    2013-12-13 15:31:03 FixMateInformation  Sorting input into queryname order.

INFO    2013-12-13 15:32:51 FixMateInformation  Sorting by queryname complete.
INFO    2013-12-13 15:32:51 FixMateInformation  Output will be sorted by coordinate
INFO    2013-12-13 15:32:51 FixMateInformation  Traversing query name sorted 
records and fixing up mate pair information.
INFO    2013-12-13 15:33:11 FixMateInformation  Processed 1000000 records.
INFO    2013-12-13 15:33:34 FixMateInformation  Processed 2000000 records.
INFO    2013-12-13 15:33:57 FixMateInformation  Processed 3000000 records.
INFO    2013-12-13 15:34:20 FixMateInformation  Processed 4000000 records.
INFO    2013-12-13 15:34:44 FixMateInformation  Processed 5000000 records.
INFO    2013-12-13 15:35:07 FixMateInformation  Processed 6000000 records.
INFO    2013-12-13 15:35:20 FixMateInformation  Finished processing reads; 
re-sorting output file.
[Fri Dec 13 15:36:51 EST 2013] net.sf.picard.sam.FixMateInformation done. 
Elapsed time: 5.81 minutes.
Runtime.totalMemory()=1457324032
\n\n!! ERROR: necessary parameters file "2013-12-13_15:27.gasv.in" does not 
exist. Ensure BAMToGASV ran correctly and restart.\n

Something is wrong. Is it because I sorted the bam file according to the 
genomic coordinates?

Original comment by jlzhuan...@gmail.com on 13 Dec 2013 at 8:44

GoogleCodeExporter commented 8 years ago 
I suspect this may have to do with the naming of chromosomes in your BAM file. 
(You'd need to use the --CHROMOSOME_NAMING_FILE option when running BAMToGASV.)

Since I received a similar comment from someone recently, I have added this to 
our troubleshooting page.

 http://code.google.com/p/gasv/wiki/Troubleshooting

Let me know if this helps.

Original comment by sora...@gmail.com on 13 Dec 2013 at 11:05

GoogleCodeExporter commented 8 years ago 
This did address the issue.

Thanks a lot!

Original comment by jlzhuan...@gmail.com on 14 Dec 2013 at 4:07

GoogleCodeExporter commented 8 years ago

Original comment by sora...@gmail.com on 27 Feb 2014 at 2:19