It gets as far as Gene Levels and Changes calculation and then dies after about 3% in with a mysql error below. I've been poking around in the t_genes_population.pl code but I can't get why this error is coming out. The select call works fine
Sean.
.... CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) WHERE chr = 'chr1' AND start >= 48771114 AND end <= 53262213 CREATE TEMPORARY TABLE CT AS SELECT * FROM V WHERE chr = 'chr1' AND start >= 53165536 AND end <= 56289870 CREATE TEMPORARY TABLE CT AS SELECT * FROM V WHERE chr = 'chr1' AND start >= 59535213 AND end <= 63000990 CREATE TEMPORARY TABLE CT AS SELECT * FROM V WHERE chr = 'chr1' AND start >= 63022391 AND end <= 66102638 CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) WHERE chr = 'chr1' AND start >= SELECT ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V WHERE () AND strand='-' AND end <= 3000000 DBD::mysql::st execute failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'SELECT ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm line 88, <$fh> line 921.
_______ =================================== Error =================================== ^^^^^^^ You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'SELECT ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' at line 3
> It gets as far as Gene Levels and Changes calculation and then dies after > about 3% in with a mysql error below. > I've been poking around in the t_genes_population.pl code but I can't get > why this error is coming out. > The select call works fine
> Sean.
> .... > CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) > WHERE chr = 'chr1' AND > start >= 48771114 AND > end <= 53262213 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 53165536 AND > end <= 56289870 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 59535213 AND > end <= 63000990 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 63022391 AND > end <= 66102638 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) > WHERE chr = 'chr1' AND > start >= SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V > WHERE () > AND strand='-' AND > end <= 3000000 > DBD::mysql::st execute failed: You have an error in your SQL syntax; check > the manual that corresponds to your MySQL server version for the right > syntax to use near 'SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' > at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm > line 88, <$fh> line 921.
> _______ > =================================== Error > =================================== > ^^^^^^^ > You have an error in your SQL syntax; check the manual that corresponds to > your MySQL server version for the right syntax to use near 'SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' > at line 3
This should have a better error message. I think it is caused by using the trimmed gene models (a few of which are empty), which should not be used for microarray studies, since microarrays can distinguish between the strands. Use hg18_gene_clusters.tsv instead of hg18_trimmed_gene_clusters.tsv.
Can you try running with the different gene clusters file and let me know if it works?
On Fri, Dec 2, 2011 at 4:09 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
> It gets as far as Gene Levels and Changes calculation and then dies after > about 3% in with a mysql error below. > I've been poking around in the t_genes_population.pl code but I can't get > why this error is coming out. > The select call works fine
> Sean.
> .... > CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) > WHERE chr = 'chr1' AND > start >= 48771114 AND > end <= 53262213 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 53165536 AND > end <= 56289870 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 59535213 AND > end <= 63000990 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V > WHERE chr = 'chr1' AND > start >= 63022391 AND > end <= 66102638 > CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) > WHERE chr = 'chr1' AND > start >= SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V > WHERE () > AND strand='-' AND > end <= 3000000 > DBD::mysql::st execute failed: You have an error in your SQL syntax; check > the manual that corresponds to your MySQL server version for the right > syntax to use near 'SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' > at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm > line 88, <$fh> line 921.
> _______ > =================================== Error > =================================== > ^^^^^^^ > You have an error in your SQL syntax; check the manual that corresponds to > your MySQL server version for the right syntax to use near 'SELECT > ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' > at line 3
> This should have a better error message. I think it is caused by using the > trimmed gene models (a few of which are empty), which should not be used > for microarray studies, since microarrays can distinguish between the > strands. Use hg18_gene_clusters.tsv instead of > hg18_trimmed_gene_clusters.tsv.
> Can you try running with the different gene clusters file and let me know > if it works?
> On Fri, Dec 2, 2011 at 4:09 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
>> Hi Brad, >> I'm trying to install a new microarray dataset into EP. I issue the call >> below:
>> It gets as far as Gene Levels and Changes calculation and then dies after >> about 3% in with a mysql error below. >> I've been poking around in the t_genes_population.pl code but I can't >> get why this error is coming out. >> The select call works fine
>> Sean.
>> .... >> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) >> WHERE chr = 'chr1' AND >> start >= 48771114 AND >> end <= 53262213 >> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >> WHERE chr = 'chr1' AND >> start >= 53165536 AND >> end <= 56289870 >> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >> WHERE chr = 'chr1' AND >> start >= 59535213 AND >> end <= 63000990 >> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >> WHERE chr = 'chr1' AND >> start >= 63022391 AND >> end <= 66102638 >> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) >> WHERE chr = 'chr1' AND >> start >= SELECT >> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V >> WHERE () >> AND strand='-' AND >> end <= 3000000 >> DBD::mysql::st execute failed: You have an error in your SQL syntax; >> check the manual that corresponds to your MySQL server version for the >> right syntax to use near 'SELECT >> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >> at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm >> line 88, <$fh> line 921.
>> _______ >> =================================== Error >> =================================== >> ^^^^^^^ >> You have an error in your SQL syntax; check the manual that corresponds >> to your MySQL server version for the right syntax to use near 'SELECT >> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >> at line 3
Actually there's now a different issue, this time with the comparisons using limma:
... ./analysis/gene_levels/gene_levels.tsv already exists. I'm going to check if it looks complete. It is not missing any of the expected fields in the header line. Let's see if it has the right number of rows---should be identical to /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv ./analysis/gene_levels/gene_levels.tsv has 26571 rows (not counting leading comment rows). Let's see about /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv has 26571 rows (not counting leading comment rows). That's the same number! I won't recalculate ./analysis/gene_levels/gene_levels.tsv. Wed Dec 7 16:45:44 EST 2011 Run(/ifs/data/columbia/tm_lab/so2346/EP_home/microarray/calculate_change_st ats_by_limma.R ./comps.txt ./analysis/gene_levels/gene_levels.tsv ./2way_comps -id clusterID -lfc_name lfc -p_name p) Loading comps [./comps.txt]... Loading genelev file [./analysis/gene_levels/gene_levels.tsv]... All samples from comps file were found in genelev file---good! genelev file has an annotation line. It will be copied to the output files: # /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv Found ID field [clusterID] in genelev file. It will be copied to the output files. Converting genelevels to matrix and taking log2... Loading required package: methods
Welcome to Bioconductor
Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'.
Constructing new ExpressionSet object... Working on comparison [All_ctrl_v_All_knockdown] Working on comparison [ctrl3_v_knockdown3] Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits Calls: eBayes -> ebayes In addition: Warning messages: 1: Zero sample variances detected, have been offset 2: Zero sample variances detected, have been offset Execution halted Non-zero exit status (1)...Exiting Wed Dec 7 16:45:51 EST 2011
On 7 December 2011 16:44, Sean O'Keeffe <limericks...@gmail.com> wrote:
> As always Brad, you have an eye for detail! > It works with the non-trimmed gene clusters. > Should I remove empty gene models for future reference?
> Sean.
> On 7 December 2011 16:19, Brad Friedman <brad.aaron.fried...@gmail.com>wrote:
>> This should have a better error message. I think it is caused by using >> the trimmed gene models (a few of which are empty), which should not be >> used for microarray studies, since microarrays can distinguish between the >> strands. Use hg18_gene_clusters.tsv instead of >> hg18_trimmed_gene_clusters.tsv.
>> Can you try running with the different gene clusters file and let me know >> if it works?
>> On Fri, Dec 2, 2011 at 4:09 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
>>> Hi Brad, >>> I'm trying to install a new microarray dataset into EP. I issue the call >>> below:
>>> It gets as far as Gene Levels and Changes calculation and then dies >>> after about 3% in with a mysql error below. >>> I've been poking around in the t_genes_population.pl code but I can't >>> get why this error is coming out. >>> The select call works fine
>>> Sean.
>>> .... >>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) >>> WHERE chr = 'chr1' AND >>> start >= 48771114 AND >>> end <= 53262213 >>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>> WHERE chr = 'chr1' AND >>> start >= 53165536 AND >>> end <= 56289870 >>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>> WHERE chr = 'chr1' AND >>> start >= 59535213 AND >>> end <= 63000990 >>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>> WHERE chr = 'chr1' AND >>> start >= 63022391 AND >>> end <= 66102638 >>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) >>> WHERE chr = 'chr1' AND >>> start >= SELECT >>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V >>> WHERE () >>> AND strand='-' AND >>> end <= 3000000 >>> DBD::mysql::st execute failed: You have an error in your SQL syntax; >>> check the manual that corresponds to your MySQL server version for the >>> right syntax to use near 'SELECT >>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>> at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm >>> line 88, <$fh> line 921.
>>> _______ >>> =================================== Error >>> =================================== >>> ^^^^^^^ >>> You have an error in your SQL syntax; check the manual that corresponds >>> to your MySQL server version for the right syntax to use near 'SELECT >>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>> at line 3
This is problem of doing a one-versus-one comparison in limma---it won't do it. You can force it to use the t-test instead, which still won't calculate P-values (and one could argue shouldn't try to anyway), but at least will give you the fold-changes so you can make plots with those. Provide the switch -dem ttest to array_pipeline.pl.
On Wed, Dec 7, 2011 at 1:54 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
> Actually there's now a different issue, this time with the comparisons > using limma:
> ... > ./analysis/gene_levels/gene_levels.tsv already exists. I'm going to check > if it looks complete. > It is not missing any of the expected fields in the header line. > Let's see if it has the right number of rows---should be identical to > /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv > ./analysis/gene_levels/gene_levels.tsv has 26571 rows (not counting > leading comment rows). > Let's see about > /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv > /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv > has 26571 rows (not counting leading comment rows). > That's the same number! I won't recalculate > ./analysis/gene_levels/gene_levels.tsv. > Wed Dec 7 16:45:44 EST 2011 > Run(/ifs/data/columbia/tm_lab/so2346/EP_home/microarray/calculate_change_st ats_by_limma.R > ./comps.txt ./analysis/gene_levels/gene_levels.tsv ./2way_comps -id > clusterID -lfc_name lfc -p_name p) > Loading comps [./comps.txt]... > Loading genelev file [./analysis/gene_levels/gene_levels.tsv]... > All samples from comps file were found in genelev file---good! > genelev file has an annotation line. It will be copied to the output files: > # > /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv > Found ID field [clusterID] in genelev file. It will be copied to the > output files. > Converting genelevels to matrix and taking log2... > Loading required package: methods
> Welcome to Bioconductor
> Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'.
> Constructing new ExpressionSet object... > Working on comparison [All_ctrl_v_All_knockdown] > Working on comparison [ctrl3_v_knockdown3] > Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim, : > No residual degrees of freedom in linear model fits > Calls: eBayes -> ebayes > In addition: Warning messages: > 1: Zero sample variances detected, have been offset > 2: Zero sample variances detected, have been offset > Execution halted > Non-zero exit status (1)...Exiting > Wed Dec 7 16:45:51 EST 2011
> On 7 December 2011 16:44, Sean O'Keeffe <limericks...@gmail.com> wrote:
>> As always Brad, you have an eye for detail! >> It works with the non-trimmed gene clusters. >> Should I remove empty gene models for future reference?
>> Sean.
>> On 7 December 2011 16:19, Brad Friedman <brad.aaron.fried...@gmail.com>wrote:
>>> This should have a better error message. I think it is caused by using >>> the trimmed gene models (a few of which are empty), which should not be >>> used for microarray studies, since microarrays can distinguish between the >>> strands. Use hg18_gene_clusters.tsv instead of >>> hg18_trimmed_gene_clusters.tsv.
>>> Can you try running with the different gene clusters file and let me >>> know if it works?
>>> On Fri, Dec 2, 2011 at 4:09 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
>>>> Hi Brad, >>>> I'm trying to install a new microarray dataset into EP. I issue the >>>> call below:
>>>> It gets as far as Gene Levels and Changes calculation and then dies >>>> after about 3% in with a mysql error below. >>>> I've been poking around in the t_genes_population.pl code but I can't >>>> get why this error is coming out. >>>> The select call works fine
>>>> Sean.
>>>> .... >>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) >>>> WHERE chr = 'chr1' AND >>>> start >= 48771114 AND >>>> end <= 53262213 >>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>> WHERE chr = 'chr1' AND >>>> start >= 53165536 AND >>>> end <= 56289870 >>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>> WHERE chr = 'chr1' AND >>>> start >= 59535213 AND >>>> end <= 63000990 >>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>> WHERE chr = 'chr1' AND >>>> start >= 63022391 AND >>>> end <= 66102638 >>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) >>>> WHERE chr = 'chr1' AND >>>> start >= SELECT >>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V >>>> WHERE () >>>> AND strand='-' AND >>>> end <= 3000000 >>>> DBD::mysql::st execute failed: You have an error in your SQL syntax; >>>> check the manual that corresponds to your MySQL server version for the >>>> right syntax to use near 'SELECT >>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>>> at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm >>>> line 88, <$fh> line 921.
>>>> _______ >>>> =================================== Error >>>> =================================== >>>> ^^^^^^^ >>>> You have an error in your SQL syntax; check the manual that corresponds >>>> to your MySQL server version for the right syntax to use near 'SELECT >>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>>> at line 3
> This is problem of doing a one-versus-one comparison in limma---it won't > do it. You can force it to use the t-test instead, which still won't > calculate P-values (and one could argue shouldn't try to anyway), but at > least will give you the fold-changes so you can make plots with those. > Provide the switch -dem ttest to array_pipeline.pl.
> On Wed, Dec 7, 2011 at 1:54 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
>> Actually there's now a different issue, this time with the comparisons >> using limma:
>> ... >> ./analysis/gene_levels/gene_levels.tsv already exists. I'm going to check >> if it looks complete. >> It is not missing any of the expected fields in the header line. >> Let's see if it has the right number of rows---should be identical to >> /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv >> ./analysis/gene_levels/gene_levels.tsv has 26571 rows (not counting >> leading comment rows). >> Let's see about >> /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv >> /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv >> has 26571 rows (not counting leading comment rows). >> That's the same number! I won't recalculate >> ./analysis/gene_levels/gene_levels.tsv. >> Wed Dec 7 16:45:44 EST 2011 >> Run(/ifs/data/columbia/tm_lab/so2346/EP_home/microarray/calculate_change_st ats_by_limma.R >> ./comps.txt ./analysis/gene_levels/gene_levels.tsv ./2way_comps -id >> clusterID -lfc_name lfc -p_name p) >> Loading comps [./comps.txt]... >> Loading genelev file [./analysis/gene_levels/gene_levels.tsv]... >> All samples from comps file were found in genelev file---good! >> genelev file has an annotation line. It will be copied to the output >> files: >> # >> /ifs/data/columbia/tm_lab/so2346/EP_home/annot/hg18/hg18_gene_clusters.tsv >> Found ID field [clusterID] in genelev file. It will be copied to the >> output files. >> Converting genelevels to matrix and taking log2... >> Loading required package: methods
>> Welcome to Bioconductor
>> Vignettes contain introductory material. To view, type >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation("pkgname")'.
>> Constructing new ExpressionSet object... >> Working on comparison [All_ctrl_v_All_knockdown] >> Working on comparison [ctrl3_v_knockdown3] >> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = >> stdev.coef.lim, : >> No residual degrees of freedom in linear model fits >> Calls: eBayes -> ebayes >> In addition: Warning messages: >> 1: Zero sample variances detected, have been offset >> 2: Zero sample variances detected, have been offset >> Execution halted >> Non-zero exit status (1)...Exiting >> Wed Dec 7 16:45:51 EST 2011
>> On 7 December 2011 16:44, Sean O'Keeffe <limericks...@gmail.com> wrote:
>>> As always Brad, you have an eye for detail! >>> It works with the non-trimmed gene clusters. >>> Should I remove empty gene models for future reference?
>>> Sean.
>>> On 7 December 2011 16:19, Brad Friedman <brad.aaron.fried...@gmail.com>wrote:
>>>> This should have a better error message. I think it is caused by using >>>> the trimmed gene models (a few of which are empty), which should not be >>>> used for microarray studies, since microarrays can distinguish between the >>>> strands. Use hg18_gene_clusters.tsv instead of >>>> hg18_trimmed_gene_clusters.tsv.
>>>> Can you try running with the different gene clusters file and let me >>>> know if it works?
>>>> On Fri, Dec 2, 2011 at 4:09 PM, Sean O'Keeffe <limericks...@gmail.com>wrote:
>>>>> Hi Brad, >>>>> I'm trying to install a new microarray dataset into EP. I issue the >>>>> call below:
>>>>> It gets as far as Gene Levels and Changes calculation and then dies >>>>> after about 3% in with a mysql error below. >>>>> I've been poking around in the t_genes_population.pl code but I can't >>>>> get why this error is coming out. >>>>> The select call works fine
>>>>> Sean.
>>>>> .... >>>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (2.92%) >>>>> WHERE chr = 'chr1' AND >>>>> start >= 48771114 AND >>>>> end <= 53262213 >>>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>>> WHERE chr = 'chr1' AND >>>>> start >= 53165536 AND >>>>> end <= 56289870 >>>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>>> WHERE chr = 'chr1' AND >>>>> start >= 59535213 AND >>>>> end <= 63000990 >>>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V >>>>> WHERE chr = 'chr1' AND >>>>> start >= 63022391 AND >>>>> end <= 66102638 >>>>> CREATE TEMPORARY TABLE CT AS SELECT * FROM V571 (3.38%) >>>>> WHERE chr = 'chr1' AND >>>>> start >= SELECT >>>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM V >>>>> WHERE () >>>>> AND strand='-' AND >>>>> end <= 3000000 >>>>> DBD::mysql::st execute failed: You have an error in your SQL syntax; >>>>> check the manual that corresponds to your MySQL server version for the >>>>> right syntax to use near 'SELECT >>>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>>>> at line 3 at /ifs/data/columbia/tm_lab/so2346/EP_home/lib/perl/EP_Mysql.pm >>>>> line 88, <$fh> line 921.
>>>>> _______ >>>>> =================================== Error >>>>> =================================== >>>>> ^^^^^^^ >>>>> You have an error in your SQL syntax; check the manual that >>>>> corresponds to your MySQL server version for the right syntax to use near >>>>> 'SELECT >>>>> ctrl_b01,ctrl_b02,ctrl_b03,siRNA_Opt_a01,siRNA_Opt_a02,siRNA_Opt_a03 FROM' >>>>> at line 3
