When visualizing a BAM dataset, Galaxy generates a bigwig dataset of read coverage. Trying to visualize this dataset is causing the issue. You could try to convert the BAM to BigWig manually (click on dataset's pencil icon --> convert format --> convert to bigwig) and see if there are any issues generating the dataset. You could then try visualizing that dataset directly to see if anything unusual happens.
Finally, there was a bug in bx-python that was fixed a while back: https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e3006c9f89b3828022ac96 if you're using an old version of Galaxy, you might try updating and see if that fixes the issue. Best, J. On Nov 22, 2013, at 8:18 AM, Shu-Yi Su <shu-yi...@embl.de> wrote: > Hi Jeremy, > > Thank you so much for reply. > You are right…..I just took the first few lines in fastq file and mapped with > bowtie. Now it works with this small dataset. > I am trying to find the error in my complete dataset, but haven't spotted any > yet. > Do you think the error is from reading the read name or position or something > else…..this could help me to dig out the error in the file? > > Thank you again for the help….without this piece of useful information, i > might had spent days and days on this : ) > > Best regards, > Shu-Yi > > On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote: > >> This appears to be an issue with the dataset that you're trying to view, not >> the build or visualization. It appears that the (bigwig? bigbed?) dataset is >> malformed in some way. Can you inspect the dataset to look for errors? Are >> you able to view a different rn5 dataset? >> >> J. >> >> On Nov 21, 2013, at 10:43 AM, Shu-Yi Su <shu-yi...@embl.de> wrote: >> >>> Hi, >>> >>> I am trying to view rat data (rn5) using trackster with data format bam or >>> bigwig on our galaxy installation, but it isn't working. It works with >>> other organisms, such as dm3 or hg19. There is error message in the log: >>> >>> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >>> /galaxy-dev/api/genomes/rn5?low=0&num=100 HTTP/1.1" 200 - >>> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >>> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >>> 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET >>> /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hda&data_type=track_config >>> HTTP/1.1" 200 - >>> "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc7104922b&hda_ldda=hda"; >>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 >>> (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" >>> galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in >>> dataset API at listing contents: 'BinaryFileReader' object has no attribute >>> 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' >>> Traceback (most recent call last): >>> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 44, in show >>> is_true( kwd.get( 'retry', False ) ) ) >>> File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 106, in _converted_datasets_state >>> if not data_provider.has_data( chrom ): >>> File >>> "/g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py", >>> line 1078, in has_data >>> all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ >>> File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query >>> (lib/bx/bbi/bbi_file.c:5596) >>> File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query >>> (lib/bx/bbi/bbi_file.c:5210) >>> File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize >>> (lib/bx/bbi/bbi_file.c:4475) >>> File "bbi_file.pyx", line 248, in >>> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) >>> File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find >>> (lib/bx/bbi/bpt_file.c:1388) >>> File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find >>> (lib/bx/bbi/bpt_file.c:1154) >>> AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' >>> >>> I also attached the first few lines in our rn5.len: >>> chr1 290094216 >>> chr2 285068071 >>> chr4 248343840 >>> chr3 183740530 >>> chr5 177180328 >>> chr6 156897508 >>> chrX 154597545 >>> chr7 143501887 >>> chr8 132457389 >>> chr9 121549591 >>> chr13 118718031 >>> chr14 115151701 >>> chr15 114627140 >>> chr10 112200500 >>> chr11 93518069 >>> chr17 92503511 >>> chr16 90051983 >>> chr18 87229863 >>> chr19 72914587 >>> chr20 57791882 >>> chr12 54450796 >>> chr4_AABR06109730_random 227955 >>> chrUn_JH620568 73090 >>> chr2_JH620298_random 62026 >>> chr5_JH620330_random 58807 >>> chrUn_JH620520 57992 >>> chrUn_JH620553 56877 >>> chr1_AABR06109393_random 52834 >>> chr18_JH620420_random 51685 >>> chr9_JH620364_random 51490 >>> chrX_JH620445_random 49212 >>> chrUn_JH620623 47760 >>> chr10_JH620371_random 44089 >>> >>> I have looked into this error for a while and still can't figure it out. >>> Any idea or suggestions are very appreciated. >>> >>> Thank you very much. >>> Best regards, >>> Shu-Yi >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >
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