Not without running it under the debugger. Since this is my program I suppose I should look at it (if you send me the file)
Phil On 17 Jan 2011, at 11:17, James Foadi wrote: > Dear CCP4ers, > does anyone understand where the problem is? The run is from the program > rebatch. > Keywords are: > > > TITLE Rebatch file for multicrystal merging > BATCH 3 TO 15 REJECT > BATCH ALL START 1 > END > > Log file follows: > > > > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > <html> <!-- CCP4 HTML LOGFILE --> > <hr> > <!--SUMMARY_END--></FONT></B> > > <a name="rebatchrebatch"><h2>REBATCH</h2></a> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > <pre> > > ############################################################### > ############################################################### > ############################################################### > ### CCP4 6.1: REBATCH version 6.1 : 17/09/08## > ############################################################### > User: unknown Run date: 17/ 1/2011 Run time: 10:55:58 > > > Please reference: Collaborative Computational Project, Number 4. 1994. > "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, > 760-763. > as well as any specific reference in the program write-up. > > <!--SUMMARY_END--></FONT></B> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > <a name="tocREBATCH"><h2>Contents</h2></a> > <ul> > <li><a href="#commandREBATCH">Command Input</a> > <li><a href="#inpREBATCH">Input MTZ File</a> > <li><a href="#outREBATCH">Output File</a> > </ul> > <hr> > > <a name="commandREBATCH"><h3>Command Input</h3></a> > <a href="/home/james/build/ccp4-6.1.13/html/rebatch.html#title">TITLE </a> > <a href="/home/james/build/ccp4-6.1.13/html/rebatch.html#batch">BATCH </a> > <a href="/home/james/build/ccp4-6.1.13/html/rebatch.html#history">HISTORY </a> > <a href="/home/james/build/ccp4-6.1.13/html/rebatch.html#detector">DETECTOR > </a> > <a href="/home/james/build/ccp4-6.1.13/html/rebatch.html#end">END</a> > <!--SUMMARY_END--></FONT></B> > <hr> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > <a name="inpREBATCH"><h3>Input MTZ File</h3></a> > <!--SUMMARY_END--></FONT></B> > > WARNING: Dataset id missing from COLUMN records in MTZ header. > WARNING: Making default dataset assignments. >>>>>>> CCP4 library signal mtz:Missing or incomplete dataset information in >>>>>>> input >>>>>>> file. (Warning) > raised in MtzGet <<<<<< > > OPENED INPUT MTZ FILE > Logical Name: HKLIN Filename: > /home/james/gwyndaf/non-isomorphism/data_for_BLEND/data/cP/d_02/sgc42-7-xds-15images.mtz > > > * Title: > > From XDS file XDS_ASCII.HKL, XDS run on 24-Apr-2009 from images images > > * Base dataset: > > 0 HKL_base > HKL_base > HKL_base > > * Number of Datasets = 1 > > * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: > > 1 XDSproject > XDScrystal > XDSdataset > 155.3040 155.3040 155.3040 90.0000 90.0000 90.0000 > 0.97780 > > * Number of Columns = 12 > > * Number of Reflections = 28622 > > * Missing value set to NaN in input mtz file > > * Number of Batches = 15 > > * Column Labels : > > H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP > > * Column Types : > > H H H Y B J Q R R R R R > > * Associated datasets : > > 0 0 0 0 0 0 0 0 0 0 0 0 > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) > > 155.3040 155.3040 155.3040 90.0000 90.0000 90.0000 > > * Resolution Range : > > 0.00025 0.08184 ( 63.372 - 3.495 A ) > > * Sort Order : > > 1 2 3 4 5 > > * Space group = 'P 2 3' (number 195) > > Data line--- TITLE Rebatch file for multicrystal merging > Data line--- BATCH 3 TO 15 REJECT > Data line--- BATCH ALL START 1 > Data line--- END > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > > List of original batch numbers and new batch numbers, = 0 if rejected > > Reflections with width greater than maximum allowed width will be rejected > > > > Old batch New batch Max allowed New project New crystal New dataset > no. no. width name name name > > 1 1 50.00 > 2 2 50.00 > 3 0 50.00 > 4 0 50.00 > 5 0 50.00 > 6 0 50.00 > 7 0 50.00 > 8 0 50.00 > 9 0 50.00 > 10 0 50.00 > 11 0 50.00 > 12 0 50.00 > 13 0 50.00 > 14 0 50.00 > 15 0 50.00 > > > > <!--SUMMARY_END--></FONT></B> > <hr> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > <a name="outREBATCH"><h3>Output File</h3></a> > <!--SUMMARY_END--></FONT></B> > *** buffer overflow detected ***: rebatch terminated > ======= Backtrace: ========= > /lib/libc.so.6(__fortify_fail+0x37)[0x2b06ab2da217] > /lib/libc.so.6(+0xfe0d0)[0x2b06ab2d90d0] > /lib/libc.so.6(+0xfd539)[0x2b06ab2d8539] > /lib/libc.so.6(__printf_fp+0x1541)[0x2b06ab227421] > /lib/libc.so.6(_IO_vfprintf+0x25fe)[0x2b06ab22299e] > /lib/libc.so.6(__vsprintf_chk+0x99)[0x2b06ab2d85d9] > /lib/libc.so.6(__sprintf_chk+0x7f)[0x2b06ab2d851f] > rebatch[0x4220d4] > rebatch[0x4084ef] > rebatch[0x408602] > rebatch[0x4060cb] > rebatch[0x406376] > rebatch[0x42b2ea] > /lib/libc.so.6(__libc_start_main+0xfd)[0x2b06ab1f9c4d] > rebatch[0x402669] > ======= Memory map: ======== > 00400000-00438000 r-xp 00000000 08:11 6701231 > /home/james/build/ccp4-6.1.13/bin/rebatch > 00638000-00639000 r--p 00038000 08:11 6701231 > /home/james/build/ccp4-6.1.13/bin/rebatch > 00639000-0063a000 rw-p 00039000 08:11 6701231 > /home/james/build/ccp4-6.1.13/bin/rebatch > 0063a000-0179d000 rw-p 00000000 00:00 0 > 032c2000-032e3000 rw-p 00000000 00:00 0 > [heap] > 2b06a9915000-2b06a9935000 r-xp 00000000 08:11 5472457 > /lib/ld-2.11.1.so > 2b06a9935000-2b06a993a000 rw-p 00000000 00:00 0 > 2b06a9b34000-2b06a9b35000 r--p 0001f000 08:11 5472457 > /lib/ld-2.11.1.so > 2b06a9b35000-2b06a9b36000 rw-p 00020000 08:11 5472457 > /lib/ld-2.11.1.so > 2b06a9b36000-2b06a9b37000 rw-p 00000000 00:00 0 > 2b06a9b37000-2b06aa42c000 r-xp 00000000 08:11 9209497 > /usr/lib/atlas/liblapack.so.3gf.0 > 2b06aa42c000-2b06aa62b000 ---p 008f5000 08:11 9209497 > /usr/lib/atlas/liblapack.so.3gf.0 > 2b06aa62b000-2b06aa62c000 r--p 008f4000 08:11 9209497 > /usr/lib/atlas/liblapack.so.3gf.0 > 2b06aa62c000-2b06aa631000 rw-p 008f5000 08:11 9209497 > /usr/lib/atlas/liblapack.so.3gf.0 > 2b06aa631000-2b06aa73e000 rw-p 00000000 00:00 0 > 2b06aa73e000-2b06aa834000 r-xp 00000000 08:11 8925829 > /usr/lib/libstdc++.so.6.0.13 > 2b06aa834000-2b06aaa34000 ---p 000f6000 08:11 8925829 > /usr/lib/libstdc++.so.6.0.13 > 2b06aaa34000-2b06aaa3b000 r--p 000f6000 08:11 8925829 > /usr/lib/libstdc++.so.6.0.13 > 2b06aaa3b000-2b06aaa3d000 rw-p 000fd000 08:11 8925829 > /usr/lib/libstdc++.so.6.0.13 > 2b06aaa3d000-2b06aaa53000 rw-p 00000000 00:00 0 > 2b06aaa53000-2b06aab3e000 r-xp 00000000 08:11 8923073 > /usr/lib/libgfortran.so.3.0.0 > 2b06aab3e000-2b06aad3d000 ---p 000eb000 08:11 8923073 > /usr/lib/libgfortran.so.3.0.0 > 2b06aad3d000-2b06aad3e000 r--p 000ea000 08:11 8923073 > /usr/lib/libgfortran.so.3.0.0 > 2b06aad3e000-2b06aad3f000 rw-p 000eb000 08:11 8923073 > /usr/lib/libgfortran.so.3.0.0 > 2b06aad3f000-2b06aad40000 rw-p 00000000 00:00 0 > 2b06aad40000-2b06aadc2000 r-xp 00000000 08:11 5472443 > /lib/libm-2.11.1.so > 2b06aadc2000-2b06aafc1000 ---p 00082000 08:11 5472443 > /lib/libm-2.11.1.so > 2b06aafc1000-2b06aafc2000 r--p 00081000 08:11 5472443 > /lib/libm-2.11.1.so > 2b06aafc2000-2b06aafc3000 rw-p 00082000 08:11 5472443 > /lib/libm-2.11.1.so > 2b06aafc3000-2b06aafd9000 r-xp 00000000 08:11 5472417 > /lib/libgcc_s.so.1 > 2b06aafd9000-2b06ab1d8000 ---p 00016000 08:11 5472417 > /lib/libgcc_s.so.1 > 2b06ab1d8000-2b06ab1d9000 r--p 00015000 08:11 5472417 > /lib/libgcc_s.so.1 > 2b06ab1d9000-2b06ab1da000 rw-p 00016000 08:11 5472417 > /lib/libgcc_s.so.1 > 2b06ab1da000-2b06ab1db000 rw-p 00000000 00:00 0 > 2b06ab1db000-2b06ab355000 r-xp 00000000 08:11 5472513 > /lib/libc-2.11.1.so > 2b06ab355000-2b06ab554000 ---p 0017a000 08:11 5472513 > /lib/libc-2.11.1.so > 2b06ab554000-2b06ab558000 r--p 00179000 08:11 5472513 > /lib/libc-2.11.1.so > 2b06ab558000-2b06ab559000 rw-p 0017d000 08:11 5472513 > /lib/libc-2.11.1.so > 2b06ab559000-2b06ab55e000 rw-p 00000000 00:00 0 > 2b06ab55e000-2b06abcef000 r-xp 00000000 08:11 9209496 > /usr/lib/atlas/libblas.so.3gf.0 > 2b06abcef000-2b06abeee000 ---p 00791000 08:11 9209496 > /usr/lib/atlas/libblas.so.3gf.0 > 2b06abeee000-2b06abef3000 r--p 00790000 08:11 9209496 > /usr/lib/atlas/libblas.so.3gf.0 > 2b06abef3000-2b06abef9000 rw-p 00795000 08:11 9209496 > /usr/lib/atlas/libblas.so.3gf.0 > 2b06abef9000-2b06abefc000 rw-p 00000000 00:00 0 > 7fffd6dd9000-7fffd6df4000 rwxp 00000000 00:00 0 > [stack] > 7fffd6df4000-7fffd6df7000 rw-p 00000000 00:00 0 > 7fffd6dff000-7fffd6e00000 r-xp 00000000 00:00 0 > [vdso] > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 > [vsyscall] > Aborted > > > > > J > > > > Dr James Foadi PhD > Membrane Protein Laboratory > Diamond Light Source Ltd. > Diamond House > Harwell Science and Innovation Campus > Didcot > Oxfordshire > OX11 0DE > United Kingdom > > > office email: james.fo...@diamond.ac.uk > alternative email: j.fo...@imperial.ac.uk > > > >
