trackster error for viewing rat data (rn5)
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
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.su@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
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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.su@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
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___________________________________________________________ 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/
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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/24893a84ce13a18815e3006... 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.su@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.su@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/
Hi, I am currently trying to use ProtK on our Galaxy installation. I have finally installed successfully ProtK on our sever by: rvm install 1.9.3 --with-gcc=clang rvm use 1.9.3 gem install protk So, I can see all the *.rb file in the bin folder (/home/base/.rvm/gems/gems/protk-1.2.5/bin/). We also have installed TPP on our sever (/g/software/src/TPP/bin/, for example). But, when i try to run tandem_search.rb on galaxy, it shows ""Could not find X!Tandem executable" (ArgumentError)" How do I let ProtK know where i installed TPP? I have spent incredible time on this to try to make it work. Any idea or suggestions are very appreciated. Thank you very much. Best Regards, Shu-Yi
participants (2)
-
Jeremy Goecks -
Shu-Yi Su