Hi Tom, It looks like the hgBbiDbLink program is failing somehow on the two files you mentioned. A couple of things you could check:
Is a corresponding row for the missing tracks appearing in the your trackDb_localTracks table? When you ran these two commands: hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized.bw hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput.bam Were the files actually present in the directory where the command was being run? It appears that hgBbiDbLink won't necessarily give an error if the file is not there. -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/24/12 1:04 PM, Maher, Thomas W wrote: > Dear Genome-Browser-Mirror Helpers, > > Love the mirror--keep up the great work. We write to request help with a > troublesome local track reinstallation effort. We were updating our mirror's > data this week when these commands were run: > > rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/gbdb/mm9/ /gbdb/mm9/ > rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/mysql/mm9/ > /var/lib/mysql/mm9/ > > ...and deleted our local tracks stored in /gbdb/mm9/bbi/, their corresponding > database tables and the trackDb_localTracks table in the mm9 database. Oops! > Not to worry, though, because we have the local track files, the trackDb.ra > file and local documentation on how to reinstall. We are running the latest > software v263 and the latest HTML. According to our local documentation, > these commands were run and should have worked to reinstall our 9 local mm9 > tracks: > > export PATH=$PATH:"~/bin/x86_64/" > export MACHTYPE="x86_64"; > export USE_BAM="1"; > export SAMDIR="/usr/local/samtools-0.1.12a"; > export MYSQLLIBS="/usr/lib64/mysql/libmysqlclient.a -lz"; > export MYSQLINC="/usr/include/mysql"; > cd ~ > mkdir gb_src_263/ > cd gb_src_263/ > wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip > unzip jksrc.zip > cd kent/src/ > make libs > cd hg > make compile > make install > cd ~/gb_src_263/kent/src/hg/makeDb/hgTrackDb/ > make > cd ../hgLoadBed/ > make > cd ../hgBbiDbLink/ > make > cd ../hgFindSpec/ > make > cd /gbdb/mm9/bbi > hgLoadBed mm9 enhancer_negative_at_e11_5 > /gbdb/mm9/bbi/enhancer_negative_at_e11_5.bed > hgLoadBed mm9 enhancer_positive_at_e11_5 > /gbdb/mm9/bbi/enhancer_positive_at_e11_5.bed > hgLoadBed mm9 FaceBase_31samps_AffyST1_0 > /gbdb/mm9/bbi/FaceBase_31samps_AffyST1_0.bed > hgLoadBed mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AWI_peaks_filtered_merged > /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AWI_peaks_filtered_merged.bed > hgLoadBed mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AWI_rejectpeaks_filtermerged > /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AWI_rejectpeaks_filtermerged.bed > hgBbiDbLink mm9 RNAseq_E13_5_palate_a /gbdb/mm9/bbi/RNAseq_E13_5_palate_a.bw > hgBbiDbLink mm9 RNAseq_E13_5_palate_b /gbdb/mm9/bbi/RNAseq_E13_5_palate_b.bw > hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized > /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized.bw > hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput > /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput.bam > hgTrackDb . mm9 trackDb_localTracks ~/gb_src_263/kent/src/hg/lib/trackDb.sql . > > NOTES: > > 1. The first 7 of 9 local tracks have installed properly and show up on > our mirror for mm9 at http://genomebrowser.facebase.org/. > 2. Two tracks: > HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized.bw and > HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput.bam do not display at all. > 3. No errors are returning from any of the commands. > 4. hgTrackDb says "Loaded 9 track descriptions total...Loaded database > mm9", as expected. > 5. For debugging purposes, all 9 track files, the trackDb.ra file and the > microarrayGroups.ra file are temporarily available here (547 MB): > http://genomebrowser.facebase.org/fbgb.tar.gz > 6. More help will be forthcoming if any more details might help. > > EXTRA NOTES: > > 1. The first two hgLoadBed commands required the full path the the bed > file, (ie. prefixed with /gbdb/mm9/bbi/)--otherwise the browser image would > display the track with a message like "No such file or directory Can't open > enhancer_negative_at_e11_5.bed to read". Curiously, the other bed files do > not require the full path in the hgLoadBed command (even though including the > full path works). Previous local track installation efforts also did not > require the full path to the local track--only that it exist in > /gbdb/mm9/bbi/. Not a problem report-just FYI. > 2. Love the browser--great work! > > Please help us get our two lost tracks back! > > Thanks, > Tom > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
