Hi Galt,
the input file I have troubles with is actually quite small, only 5.1K.
It's attached.
The thing is, when I delete the last region from the file then it works,
but I can't see anything wrong with the last region and bedToBigBed
doesn't complain either, it just keeps running. (command: ./bedToBigBed
infinite_loop.bed hsa_chromosome_sizes.txt out.bb)
Regards,
Thomas
Am 25.07.2012 03:08, schrieb Galt Barber:
Hi, Thomas!
You can send it to me: galt soe.ucsc.edu <http://soe.ucsc.edu>
It won't receive attachments over 25MB.
If you can put it on some server and send me the URL,
that would be helpful.
-Galt
On Tue, Jul 24, 2012 at 5:47 AM, Thomas Blank
<[email protected] <mailto:[email protected]>> wrote:
Hello,
I tried to convert a BED file into a bigBed file using the bedToBigBed
executable from
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/,
but bedToBigBed doesn't return a result it just keeps running. When
using other input data it works fine. Can someone take a look at this?
(To whom shall I send the input BED file? Sending it to the
mailing list
wouldn't work, would it?)
Regards,
--
Thomas Blank
Genomatix Software GmbH
Bayerstr. 85a
80335 Muenchen/Germany
phone: +49 89 599766-0 <tel:%2B49%2089%20599766-0>
http://www.genomatix.de
Legal information: HRB 117956, Amtsgericht Muenchen; Tax-ID: DE
189568720
Managing Directors: Dr. Matthias Scherf (COO), Dr. Martin Seifert
(CEO)
_______________________________________________
Genome maillist - [email protected] <mailto:[email protected]>
https://lists.soe.ucsc.edu/mailman/listinfo/genome
--
Thomas Blank
Genomatix Software GmbH
Bayerstr. 85a
80335 Muenchen/Germany
phone: +49 89 599766-0
http://www.genomatix.de
Legal information: HRB 117956, Amtsgericht Muenchen; Tax-ID: DE 189568720
Managing Directors: Dr. Matthias Scherf (COO), Dr. Martin Seifert (CEO)
#Organism: hsa
#Chromosome Start End
chr1 20739147 20755076
chr1 21324126 21327691
chr1 21324126 21327691
chr1 21324126 21327691
chr1 21324126 21327691
chr1 21324126 21327691
chr1 21324126 21327691
chr1 21324126 21327691
chr1 24973699 24975349
chr1 24973699 24975349
chr1 24973699 24975349
chr1 24973699 24975349
chr1 24973699 24975349
chr1 24973699 24975349
chr1 34329778 34329863
chr1 34329778 34329863
chr1 34329778 34329863
chr1 34329778 34329863
chr1 34329778 34329863
chr1 43850350 43850636
chr1 85115631 85116044
chr1 85115631 85116044
chr1 90171959 90178267
chr1 90171959 90178267
chr1 90171959 90178267
chr1 112289582 112290112
chr1 112289582 112290112
chr1 145508029 145508146
chr1 145508029 145508146
chr1 145508029 145508146
chr1 156697600 156698206
chr1 178062547 178062695
chr1 179335261 179335538
chr1 179335261 179335538
chr1 179335261 179335538
chr1 225705692 225706899
chr1 225705692 225706899
chr1 225705692 225706899
chr1 228278772 228284778
chr1 243328088 243331588
chr1 243328088 243331588
chr1 243328088 243331588
chr1 243328088 243331588
chr1 243328088 243331588
chr1 243328088 243331588
chr1 243328088 243331588
chr10 127438097 127439008
chr10 127438097 127439008
chr10 127697835 127697941
chr10 127697835 127697941
chr10 127697835 127697941
chr10 127697835 127697941
chr10 127697835 127697941
chr11 32124704 32124826
chr11 50274767 50280084
chr11 50274767 50280084
chr11 50274767 50280084
chr11 74618318 74620933
chr11 89939440 89939915
chr11 96121993 96122528
chr11 130106111 130106687
chr12 18866759 18872364
chr12 40918909 40919184
chr12 40919232 40920074
chr12 40919423 40920074
chr12 40919423 40920074
chr12 40919423 40920074
chr12 40919423 40920074
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 45951350 64316484
chr13 77844673 77846457
chr13 98612512 98612600
chr14 21500539 21503952
chr14 104027529 104028249
chr17 6527326 6528074
chr17 6527326 6528074
chr17 6527326 6528074
chr17 6527326 6528074
chr17 15343599 15355826
chr17 37566639 37566833
chr17 46925819 46926615
chr17 46925819 46926615
chr19 2427044 2427253
chr19 2427044 2427253
chr19 2427044 2427253
chr19 2427044 2427253
chr19 14218221 14232343
chr19 14218221 14232343
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 86831486 86844298
chr2 96604649 96604734
chr2 110362510 110370997
chr2 110362510 110370997
chr2 110362510 110370997
chr2 110362510 110370997
chr2 110362510 110370997
chr2 135625309 135626513
chr2 233633115 233651859
chr2 233653300 233655425
chr20 8000751 8001037
chr20 8000751 8001037
chr20 18326190 18328128
chr21 40763762 40777839
chr21 45928812 45929134
chr21 45928812 45929134
chr21 45928812 45929134
chr21 45928812 45929134
chr21 45928812 45929134
chr21 45928812 45929134
chr21 45928812 45929134
chr22 26839518 26853824
chr22 39035729 39045949
chr22 39871944 39872462
chr22 41998787 41999262
chr22 41998787 41999262
chr22 41998787 41999262
chr3 15709812 15711616
chr3 86996217 87017739
chr3 86996217 87017739
chr3 86996217 87017739
chr3 86996217 87017739
chr3 86996217 87017739
chr3 86996217 87017739
chr3 111821812 111830738
chr3 114592955 114619150
chr3 114592955 114619150
chr3 114592955 114619150
chr3 123665904 123666126
chr3 141820683 141884479
chr3 169795711 169797561
chr4 4473433 4480393
chr4 17806379 17806729
chr4 100125588 100195281
chr4 155666018 155669340
chr5 892478 894901
chr5 892478 894901
chr5 892478 894901
chr5 892478 894901
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 55243417 55244725
chr5 96109050 96112571
chr5 96109050 96112571
chr6 4126353 4130375
chr6 31779762 31782665
chr6 41088396 41089084
chr6 41107943 41108335
chr6 41107943 41108335
chr6 41107943 41108335
chr6 135813429 135816676
chr7 5781275 5781378
chr7 5781275 5781378
chr7 5781275 5781378
chr7 5781275 5781378
chr7 36397199 36407808
chr7 72397501 76063354
chr7 87913224 87921502
chr7 87913224 87921502
chr7 87913224 87921502
chr7 87913224 87921502
chr7 91874448 91875103
chr7 91874448 91875103
chr7 91874448 91875103
chr7 92086903 92090632
chr7 92086903 92090632
chr7 106815190 106820261
chr7 107333504 107333996
chr7 107333504 107333996
chr7 107333504 107333996
chr7 107333504 107333996
chr8 10355481 10356237
chr8 28906878 28907718
chr9 3488892 3490278
chr9 3488892 3490278
chr9 100700502 100707049
chr9 100700502 100707049
chr9 100700502 100707049
chr9 100700502 100707049
chrX 53115492 53116957
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr19 59128983
chr1 249250621
chr20 63025520
chr21 48129895
chr22 51304566
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chr8 146364022
chr9 141213431
chrMT 16571
chrX 155270560
chrY 59373566
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
