Seems unlikely to be due to your input file.
I'll have somebody look into it.
-Galt
Gordon Robertson wrote:
> Galt
>
> Let me get back to you on 'libs' shortly. Could I ask first about a
> bedToBigBed error message?
>
> The input bed file is 1,013,372 records, and has no track line header.
> Records are of this format:
> chr1 137005859 137005861 d_2_c
>
> I sorted the bed file following bedToBigBed's warning -
> sort -k1,1 -k2,2n $BED > $SORTEDBED
>
> Then,
> {xhost06}/projects/morgen/wtss_assembly/resources/tass_db_2>
> ./tass_db_2_bedToBigBed.sh
> pass1 - making usageList (32 chroms): 834 millis
> pass2 - checking and writing primary data (1013372 records, 4 fields): 2799
> millis
> index write: 1 millis
> bedToBigBed: bedToBigBed.c:394: writeReducedOnceReturnReducedTwice: Assertion
> `boundsPt == boundsEnd' failed.
> ./tass_db_2_bedToBigBed.sh: line 13: 14201 Aborted
> bedToBigBed $SORTEDBED $SIZES $DIR/my.bb
>
> At the point where the error was reported, the bigBed output file was 5.1 MB.
>
> Is the error likely due to a problem in my bed file?
>
> Thanks for your help -
>
> Gordon
>
>
> On 2010-02-01, at 1:04 PM, Galt Barber wrote:
>
>> Very close there.
>> Please try "make libs" instead of "make lib".
>>
>> Then you should be able to get raSqlQuery etc to compile.
>>
>> -Galt
>>
>> Gordon Robertson wrote:
>>> Thanks for your quick response, Galt.
>>> I changed 'X*Y' to '(X*Y)', exported what worked in the past -
>>> export MACHTYPE=x86_64
>>> export MYSQLINC=-I/usr/include/mysql
>>> export MYSQLLIBS='-L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm
>>> -L/usr/lib64 -lssl -lcrypto'
>>> ...and ran 'make' from the src/utils folder. Many (!) tools compiled. The
>>> following error was reported, probably because I've not done all earlier
>>> steps correctly -
>>> make[1]: *** No rule to make target `../../lib/x86_64/jkhgap.a', needed by
>>> `raSqlQuery'. Stop.
>>> make[1]: Leaving directory
>>> `/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/raSqlQuery'
>>> make: *** [all] Error 2
>>> Could you clarify this error? I'd compiled lib -
>>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src> make lib
>>> make: Nothing to be done for `lib'.
>>> ...but jkjgap.a is not in this folder -
>>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/lib/x86_64> ll
>>> total 6284
>>> -rw-rw-r-- 1 grobertson users 893 Jan 30 18:24 jkOwnLib.a
>>> -rw-rw-r-- 1 grobertson users 5370 Jan 30 18:24 jkweb.a
>>> -rwxrwxr-x 1 grobertson users 0 Dec 1 2006 placeHolder.c
>>> ---
>>> I now have bedToBigBed, which was the original goal -
>>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed>
>>> bedToBigBed ./test.bed ./chrom.sizes ./out.bb pass1 - making usageList (3
>>> chroms): 21 millis
>>> pass2 - checking and writing primary data (12 records, 4 fields): 1 millis
>>> index write: 0 millis
>>> pass3 - writeReducedOnceReturnReducedTwice: 1 millis
>>> further reductions: 0 millis
>>> Thanks again.
>>> G
>>> On 2010-02-01, at 12:00 PM, [email protected] wrote:
>>>> Message: 4
>>>> Date: Mon, 01 Feb 2010 11:20:38 -0800
>>>> From: Galt Barber <[email protected]>
>>>> Subject: Re: [Genome] can't compile bedToBigBed on RHELinux 4.x?
>>>> To: Gordon Robertson <[email protected]>
>>>> Cc: [email protected]
>>>> Message-ID: <[email protected]>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> Hi, Gordon!
>>>>
>>>> Looks like you are using gcc 3.4
>>>> and we are using gcc 4.1.2 on 64-bit linux.
>>>>
>>>> Either the gcc3.4 is more sensitive
>>>> and gcc4 has a bug in not showing the
>>>> warning; or, perhaps the gcc developers
>>>> decided that this shouldn't be a warning after all.
>>>>
>>>> In any case, simply adding parentheses around the
>>>> argument made both compilers happy.
>>>>
>>>> bits64 is definted as unsigned long long.
>>>>
>>>> In effect we had this:
>>>>
>>>> printf("%llu", (bits64)X*Y);
>>>>
>>>> and both versions of gcc are happy when we changed it to
>>>>
>>>> printf("%llu", (bits64)(X*Y));
>>>>
>>>> This change has been commmitted.
>>>> You can either update this file from CVS
>>>> or else you can just add the parentheses yourself.
>>>>
>>>> -Galt
>>>>
>>>> Gordon Robertson wrote:
>>>>> Is there a problem with the current Kent source tree bedToBigBed?
>>>>> I downloaded jksrc.zip tonight to 64-bit Red Hat Enterprise Linux 4.x.
>>>>> I'd been using wigToBigWig for some time on that machine, but wanted to
>>>>> ensure that I was using the latest version. I recompiled it after cd'ing
>>>>> to the src/utils/wigToBigWig folder -
>>>>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/wigToBigWig> make
>>>>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type
>>>>> -Wuninitialized -o /home/grobertson/bin/x86_64/wigToBigWig wigToBigWig.o
>>>>> ../../lib/x86_64/jkweb.a -lm -lz
>>>>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/wigToBigWig>
>>>>> wigToBigWig
>>>>> wigToBigWig v 3 - Convert ascii format wig file (in fixedStep,
>>>>> variableStep
>>>>> or bedGraph format) to binary big wig format.
>>>>> ...
>>>>>
>>>>> I want to start to use bedToBigBed. When I ran make from the src/utils
>>>>> folder, a number of folders were processed (aNotB, addCols, ave, aveCols,
>>>>> bedClip, bedGraphToBigWig) but there was an error message for bedToBigBed
>>>>> -
>>>>> make[1]: Entering directory
>>>>> `/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed'
>>>>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type
>>>>> -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
>>>>> -DMACHTYPE_x86_64 -Wall -Werror -Wformat -Wimplicit -Wreturn-type
>>>>> -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc
>>>>> -I../../../../../inc -o bedToBigBed.o -c bedToBigBed.c
>>>>> bedToBigBed.c: In function `bbFileCreate':
>>>>> bedToBigBed.c:537: warning: long long unsigned int format, long unsigned
>>>>> int arg (arg 4)
>>>>> make[1]: *** [bedToBigBed.o] Error 1
>>>>> make[1]: Leaving directory
>>>>> `/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed'
>>>>> make: *** [all] Error 2
>>>>>
>>>>> If I'm missing something simple I apologize for wasting the list's time.
>>>>> Thanks for your help with this.
>>>>>
>>>>> Gordon
>>> --
>>> Gordon Robertson
>>> BC Cancer Agency Genome Sciences Centre
>>> Vancouver BC Canada
>>> _______________________________________________
>>> Genome maillist - [email protected]
>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
> --
> Gordon Robertson
> BC Cancer Agency Genome Sciences Centre
> Vancouver BC Canada
>
>
>
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