Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
Hi, I'm having the same issue, has it been fixed since then? Thanks, L-A Le 07/11/2011 21:43, Nate Coraor a écrit : On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote: Hi, Reading a little more about this problem, I see Galaxy uses python tempfile library (http://docs.python.org/library/tempfile.html), specifically at line 70 in tools/samtools/sam_to_bam.py: tmp_dir = tempfile.mkdtemp() mkdtemp should honor TMPDIR, TEMP or TMP environment variables, I setup all tree of them in "~/.bashrc" with no results. I'm using: "default_cluster_job_runner = drmaa://-q all.q -V/" With "-V" I was hoping to be able to export all my environment variables, which seems to work for everything else, but not for the TMP. I ended hardcoding the "dir" argument, which is not good workaround, as I'm guessing this is not the only tool that will run into this problem: tmp_dir = tempfile.mkdtemp( dir='/home/cborroto/galaxy_dist/database/tmp') Any advice? In a more SGE related question, is there a way for me to debug what environment I'm getting when running Galaxy jobs? Hi Carlos, Try submitting an SGE job from the command line and having a look at the environment variables set on the execution host. Most likely, SGE is setting its own TMPDIR variable which would be overriding the value set with -V. --nate Thanks, Carlos On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto wrote: Hi Jen, Thanks for the quick response. The workaround you describe could work, but I might run into trouble later on. My interest is to develop a workflow for GATK, which have very strict requirements on the input BAM file. One of which is that the sorting have to be exactly the same as the reference. My reference is not sorted lexicographically "chr1, chr10, chr11, ", but instead is sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to do this with "Filter and Sort -> Sort". Also GATK needs the header for the @RG tags, which I could resolve by just reintroducing the header later on, but still it will be cumbersome. I'll work on my galaxy/cluster configuration and see if I can find why the SAM-to-BAM tool is failing. Thanks again, Carlos On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson wrote: Hello Carlos, If what you want is a sorted SAM file, then the tool "Filter and Sort -> Sort" may be a better choice. A SAM file is a tabular file. If there is header data at the beginning of the SAM file, it can be removed before running Sort with the tool "Filter and Sort -> Select" (with a "not" matching regex). Although, you can choose to not include header output as a BWA option. Perhaps this will solve the immediate problem? Best, Jen Galaxy team On 11/3/11 12:43 PM, Carlos Borroto wrote: Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_)," When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/ ___ 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/ ___
Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote: > Hi, > > Reading a little more about this problem, I see Galaxy uses python > tempfile library (http://docs.python.org/library/tempfile.html), > specifically at line 70 in tools/samtools/sam_to_bam.py: > tmp_dir = tempfile.mkdtemp() > > mkdtemp should honor TMPDIR, TEMP or TMP environment variables, I > setup all tree of them in "~/.bashrc" with no results. I'm using: > "default_cluster_job_runner = drmaa://-q all.q -V/" > > With "-V" I was hoping to be able to export all my environment > variables, which seems to work for everything else, but not for the > TMP. > > I ended hardcoding the "dir" argument, which is not good workaround, > as I'm guessing this is not the only tool that will run into this > problem: > tmp_dir = tempfile.mkdtemp( dir='/home/cborroto/galaxy_dist/database/tmp') > > Any advice? In a more SGE related question, is there a way for me to > debug what environment I'm getting when running Galaxy jobs? Hi Carlos, Try submitting an SGE job from the command line and having a look at the environment variables set on the execution host. Most likely, SGE is setting its own TMPDIR variable which would be overriding the value set with -V. --nate > > Thanks, > Carlos > > On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto > wrote: >> Hi Jen, >> >> Thanks for the quick response. The workaround you describe could work, >> but I might run into trouble later on. >> >> My interest is to develop a workflow for GATK, which have very strict >> requirements on the input BAM file. One of which is that the sorting >> have to be exactly the same as the reference. My reference is not >> sorted lexicographically "chr1, chr10, chr11, ", but instead is >> sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to >> do this with "Filter and Sort -> Sort". Also GATK needs the header for >> the @RG tags, which I could resolve by just reintroducing the header >> later on, but still it will be cumbersome. >> >> I'll work on my galaxy/cluster configuration and see if I can find why >> the SAM-to-BAM tool is failing. >> >> Thanks again, >> Carlos >> >> On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson wrote: >>> >>> Hello Carlos, >>> >>> If what you want is a sorted SAM file, then the tool "Filter and Sort -> >>> Sort" may be a better choice. A SAM file is a tabular file. >>> >>> If there is header data at the beginning of the SAM file, it can be removed >>> before running Sort with the tool "Filter and Sort -> Select" (with a "not" >>> matching regex). Although, you can choose to not include header output as a >>> BWA option. >>> >>> Perhaps this will solve the immediate problem? >>> >>> Best, >>> >>> Jen >>> Galaxy team >>> >>> On 11/3/11 12:43 PM, Carlos Borroto wrote: Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_)," When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos ___ 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/ >>> >>> -- >>> Jennifer Jackson >>> http://usegalaxy.org >>> http://galaxyproject.org/wiki/Support >>> >> > > ___ > 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/ > _
Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
Hi, Reading a little more about this problem, I see Galaxy uses python tempfile library (http://docs.python.org/library/tempfile.html), specifically at line 70 in tools/samtools/sam_to_bam.py: tmp_dir = tempfile.mkdtemp() mkdtemp should honor TMPDIR, TEMP or TMP environment variables, I setup all tree of them in "~/.bashrc" with no results. I'm using: "default_cluster_job_runner = drmaa://-q all.q -V/" With "-V" I was hoping to be able to export all my environment variables, which seems to work for everything else, but not for the TMP. I ended hardcoding the "dir" argument, which is not good workaround, as I'm guessing this is not the only tool that will run into this problem: tmp_dir = tempfile.mkdtemp( dir='/home/cborroto/galaxy_dist/database/tmp') Any advice? In a more SGE related question, is there a way for me to debug what environment I'm getting when running Galaxy jobs? Thanks, Carlos On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto wrote: > Hi Jen, > > Thanks for the quick response. The workaround you describe could work, > but I might run into trouble later on. > > My interest is to develop a workflow for GATK, which have very strict > requirements on the input BAM file. One of which is that the sorting > have to be exactly the same as the reference. My reference is not > sorted lexicographically "chr1, chr10, chr11, ", but instead is > sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to > do this with "Filter and Sort -> Sort". Also GATK needs the header for > the @RG tags, which I could resolve by just reintroducing the header > later on, but still it will be cumbersome. > > I'll work on my galaxy/cluster configuration and see if I can find why > the SAM-to-BAM tool is failing. > > Thanks again, > Carlos > > On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson wrote: >> >> Hello Carlos, >> >> If what you want is a sorted SAM file, then the tool "Filter and Sort -> >> Sort" may be a better choice. A SAM file is a tabular file. >> >> If there is header data at the beginning of the SAM file, it can be removed >> before running Sort with the tool "Filter and Sort -> Select" (with a "not" >> matching regex). Although, you can choose to not include header output as a >> BWA option. >> >> Perhaps this will solve the immediate problem? >> >> Best, >> >> Jen >> Galaxy team >> >> On 11/3/11 12:43 PM, Carlos Borroto wrote: >>> >>> Hi, >>> >>> I'm running into this error: >>> "Error sorting alignments from >>> (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_)," >>> >>> When using SAM-to-BAM tool on a locally install Galaxy using a SGE >>> cluster. I'm using the last version of galaxy-dist. I'm guessing I >>> have a problem with the configuration for the tmp folder. I have this >>> on "universe_wsgi.ini": >>> # Temporary files are stored in this directory. >>> new_file_path = /home/cborroto/galaxy_dist/database/tmp >>> >>> But I don't see this directory being used and from the error looks >>> like /tmp in the node is used. I wonder if this is the problem, as I >>> don't know if there is enough space in the local /tmp directory at the >>> nodes? I ran the same tool in a subset of the same SAM file and it ran >>> fine. >>> >>> Also, I see this in the description of the tool: >>> "This tool uses the SAMTools toolkit to produce an indexed BAM file >>> based on a sorted input SAM file." >>> >>> But what I actually need is to sort a SAM file output from bwa, I >>> haven't found any other way than to converting it to BAM. Looking at >>> "sam_to_bam.py" I see the BAM file will also be sorted. Would it be >>> wrong to feed an unsorted SAM file into this tool? >>> >>> Finally, just to be sure there is nothing wrong with the initial SAM >>> file, I ran "samtools view ..." and "samtools sort ..." on this file >>> manually outside of Galaxy and it ran fine. >>> >>> Thanks in advance, >>> Carlos >>> ___ >>> 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/ >> >> -- >> Jennifer Jackson >> http://usegalaxy.org >> http://galaxyproject.org/wiki/Support >> > ___ 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/
Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
Hi Jen, Thanks for the quick response. The workaround you describe could work, but I might run into trouble later on. My interest is to develop a workflow for GATK, which have very strict requirements on the input BAM file. One of which is that the sorting have to be exactly the same as the reference. My reference is not sorted lexicographically "chr1, chr10, chr11, ", but instead is sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to do this with "Filter and Sort -> Sort". Also GATK needs the header for the @RG tags, which I could resolve by just reintroducing the header later on, but still it will be cumbersome. I'll work on my galaxy/cluster configuration and see if I can find why the SAM-to-BAM tool is failing. Thanks again, Carlos On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson wrote: > > Hello Carlos, > > If what you want is a sorted SAM file, then the tool "Filter and Sort -> > Sort" may be a better choice. A SAM file is a tabular file. > > If there is header data at the beginning of the SAM file, it can be removed > before running Sort with the tool "Filter and Sort -> Select" (with a "not" > matching regex). Although, you can choose to not include header output as a > BWA option. > > Perhaps this will solve the immediate problem? > > Best, > > Jen > Galaxy team > > On 11/3/11 12:43 PM, Carlos Borroto wrote: >> >> Hi, >> >> I'm running into this error: >> "Error sorting alignments from >> (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_)," >> >> When using SAM-to-BAM tool on a locally install Galaxy using a SGE >> cluster. I'm using the last version of galaxy-dist. I'm guessing I >> have a problem with the configuration for the tmp folder. I have this >> on "universe_wsgi.ini": >> # Temporary files are stored in this directory. >> new_file_path = /home/cborroto/galaxy_dist/database/tmp >> >> But I don't see this directory being used and from the error looks >> like /tmp in the node is used. I wonder if this is the problem, as I >> don't know if there is enough space in the local /tmp directory at the >> nodes? I ran the same tool in a subset of the same SAM file and it ran >> fine. >> >> Also, I see this in the description of the tool: >> "This tool uses the SAMTools toolkit to produce an indexed BAM file >> based on a sorted input SAM file." >> >> But what I actually need is to sort a SAM file output from bwa, I >> haven't found any other way than to converting it to BAM. Looking at >> "sam_to_bam.py" I see the BAM file will also be sorted. Would it be >> wrong to feed an unsorted SAM file into this tool? >> >> Finally, just to be sure there is nothing wrong with the initial SAM >> file, I ran "samtools view ..." and "samtools sort ..." on this file >> manually outside of Galaxy and it ran fine. >> >> Thanks in advance, >> Carlos >> ___ >> 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > ___ 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/
Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
> ___ > 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/ Hello Carlos, If what you want is a sorted SAM file, then the tool "Filter and Sort -> Sort" may be a better choice. A SAM file is a tabular file. If there is header data at the beginning of the SAM file, it can be removed before running Sort with the tool "Filter and Sort -> Select" (with a "not" matching regex). Although, you can choose to not include header output as a BWA option. Perhaps this will solve the immediate problem? Best, Jen Galaxy team On 11/3/11 12:43 PM, Carlos Borroto wrote: Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_)," When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
[galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster
Hi, I'm running into this error: "Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), " When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp folder. I have this on "universe_wsgi.ini": # Temporary files are stored in this directory. new_file_path = /home/cborroto/galaxy_dist/database/tmp But I don't see this directory being used and from the error looks like /tmp in the node is used. I wonder if this is the problem, as I don't know if there is enough space in the local /tmp directory at the nodes? I ran the same tool in a subset of the same SAM file and it ran fine. Also, I see this in the description of the tool: "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." But what I actually need is to sort a SAM file output from bwa, I haven't found any other way than to converting it to BAM. Looking at "sam_to_bam.py" I see the BAM file will also be sorted. Would it be wrong to feed an unsorted SAM file into this tool? Finally, just to be sure there is nothing wrong with the initial SAM file, I ran "samtools view ..." and "samtools sort ..." on this file manually outside of Galaxy and it ran fine. Thanks in advance, Carlos ___ 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/
