search

glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
Other
80 stars 26 forks source link

about running progressivecatus #18

Open leirhyh opened 10 years ago

leirhyh commented 10 years ago

Hi, Glenn: I installed the progressivecactus on my new computer with Linux operation system. When I run both my data and the test data, I meet an error such as RuntimeError: Unable to launch ktserver.

Could you please help me fix this issue?

Thanks a bunch,

All the best,

Runhua

joelarmstrong commented 10 years ago

Hi, Could you please copy and paste the cactus.log file from your progressiveCactus work dir?

For example, if you are running with runProgressiveCactus.sh seqFile.txt work/ output.hal the file would be work/cactus.log.

Thanks!

leirhyh commented 10 years ago

Hi, there: Please see the attachment of the Cactus.log in attachment. All the best,

Runhua

On Thu, Apr 17, 2014 at 2:15 PM, Joel Armstrong notifications@github.comwrote:

Hi, Could you please copy and paste the cactus.log file from your progressiveCactus work dir?

For example, if you are running with runProgressiveCactus.sh seqFile.txt work/ output.hal the file would be work/cactus.log.

Thanks!

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-40751664 .

joelarmstrong commented 10 years ago

Sorry, I think the attachment didn't work since it got sent by email to github. Could you send it to jcarmstr@ucsc.edu, or paste it in the github issue?

Thanks!

leirhyh commented 10 years ago

Hi, Joel: Please see the cactus.log as follows. Thanks, Runhua

2014-04-16 12:22:38.325192: Beginning Progressive Cactus Alignment Got message from job at time: 1397668959.47 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mar55.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mar55.fa Total-sequences: 134774 Total-length: 21412782 Proportion-repeat-masked: 0.000308 ProportionNs: 0.000308 N50: 0 Median-sequence-length: 144 Got message from job at time: 1397668960.16 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/rano217.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/rano217.fa Total-sequences: 229100 Total-length: 41765894 Proportion-repeat-masked: 0.000220 ProportionNs: 0.000220 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397668960.2 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/bema8.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/bema8.fa Total-sequences: 237877 Total-length: 44125254 Proportion-repeat-masked: 0.000207 ProportionNs: 0.000207 N50: 0 Median-sequence-length: 156 Got message from job at time: 1397668960.36 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/nofy610.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/nofy610.fa Total-sequences: 272528 Total-length: 51925339 Proportion-repeat-masked: 0.000177 ProportionNs: 0.000177 N50: 0 Median-sequence-length: 153 Got message from job at time: 1397668961.17 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/dasi523.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/dasi523.fa Total-sequences: 155896 Total-length: 25711621 Proportion-repeat-masked: 0.000286 ProportionNs: 0.000286 N50: 0 Median-sequence-length: 147 Got message from job at time: 1397668961.21 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/tafo69.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/tafo69.fa Total-sequences: 277313 Total-length: 49938213 Proportion-repeat-masked: 0.000143 ProportionNs: 0.000143 N50: 0 Median-sequence-length: 142 Got message from job at time: 1397668961.54 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mas66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mas66.fa Total-sequences: 221282 Total-length: 40013045 Proportion-repeat-masked: 0.000232 ProportionNs: 0.000232 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397668962.08 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/fan66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/fan66.fa Total-sequences: 277502 Total-length: 52675079 Proportion-repeat-masked: 0.000166 ProportionNs: 0.000166 N50: 0 Median-sequence-length: 150 Got message from job at time: 1397668962.25 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/m155.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/m155.fa Total-sequences: 115604 Total-length: 18319508 Proportion-repeat-masked: 0.000285 ProportionNs: 0.000285 N50: 0 Median-sequence-length: 143 Got message from job at time: 1397668962.99 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/and34.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/and34.fa Total-sequences: 285209 Total-length: 54341263 Proportion-repeat-masked: 0.000165 ProportionNs: 0.000165 N50: 0 Median-sequence-length: 149 Got message from job at time: 1397668963.11 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/ranol61.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/ranol61.fa Total-sequences: 328828 Total-length: 58321330 Proportion-repeat-masked: 0.000136 ProportionNs: 0.000136 N50: 0 Median-sequence-length: 128 Got message from job at time: 1397669384.56 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_mar55.fa Total-sequences: 134774 Total-length: 21412782 Proportion-repeat-masked: 0.003630 ProportionNs: 0.000308 N50: 0 Median-sequence-length: 144 Got message from job at time: 1397669448.03 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_rano217.fa Total-sequences: 229100 Total-length: 41765894 Proportion-repeat-masked: 0.005052 ProportionNs: 0.000220 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397669451.07 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_bema8.fa Total-sequences: 237877 Total-length: 44125254 Proportion-repeat-masked: 0.005676 ProportionNs: 0.000207 N50: 0 Median-sequence-length: 156 Got message from job at time: 1397669452.88 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_dasi523.fa Total-sequences: 155896 Total-length: 25711621 Proportion-repeat-masked: 0.004171 ProportionNs: 0.000286 N50: 0 Median-sequence-length: 147 Got message from job at time: 1397669455.23 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_nofy610.fa Total-sequences: 272528 Total-length: 51925339 Proportion-repeat-masked: 0.006137 ProportionNs: 0.000177 N50: 0 Median-sequence-length: 153 Got message from job at time: 1397669455.23 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_m155.fa Total-sequences: 115604 Total-length: 18319508 Proportion-repeat-masked: 0.005549 ProportionNs: 0.000285 N50: 0 Median-sequence-length: 143 Got message from job at time: 1397669457.93 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_mas66.fa Total-sequences: 221282 Total-length: 40013045 Proportion-repeat-masked: 0.005201 ProportionNs: 0.000232 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397669458.59 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_tafo69.fa Total-sequences: 277313 Total-length: 49938213 Proportion-repeat-masked: 0.005126 ProportionNs: 0.000143 N50: 0 Median-sequence-length: 142 Got message from job at time: 1397669458.88 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_and34.fa Total-sequences: 285209 Total-length: 54341263 Proportion-repeat-masked: 0.006265 ProportionNs: 0.000164 N50: 0 Median-sequence-length: 149 Got message from job at time: 1397669459.05 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_fan66.fa Total-sequences: 277502 Total-length: 52675079 Proportion-repeat-masked: 0.006250 ProportionNs: 0.000166 N50: 0 Median-sequence-length: 150 Got message from job at time: 1397669462.75 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_ranol61.fa Total-sequences: 328828 Total-length: 58321330 Proportion-repeat-masked: 0.006059 ProportionNs: 0.000136 N50: 0 Median-sequence-length: 128 Got message from job at time: 1397669463.27 : The longest path in the tree is 0.385017 Got message from job at time: 1397669463.27 : Made argument lastzArguments=--step=1 --ambiguous=iupac,100 --ydrop=3000 in tag caf with divergence threshold of 9223372036854775807 for longest path of 0.38501709 (useDefaultDivergences=False) The job seems to have left a log file, indicating failure: /software/progressiveCactus/lemur/jobTree/jobs/t0/job Reporting file: /software/progressiveCactus/lemur/jobTree/jobs/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/software/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/software/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/software/progressiveCactus/submodules/cactus/pipeline/ktserverJobTree.py", line 139, in run log.txt: killPingInterval=self.runTimestep) log.txt: File "/software/progressiveCactus/submodules/cactus/pipeline/ktserverControl.py", line 130, in runKtserver log.txt: raise e log.txt: RuntimeError: Unable to launch ktserver. Server log is: /software/progressiveCactus/lemur/progressiveAlignment/Anc09/Anc09/Anc09_DB/ktout.log log.txt: Exiting the slave because of a failed job on host genetics2 log.txt: Due to failure we are reducing the remaining retry count of job /software/progressiveCactus/lemur/jobTree/jobs/t0/job to 0 log.txt: We have set the default memory of the failed job to 34359738368 bytes Job: /software/progressiveCactus/lemur/jobTree/jobs/t0/job is completely failed

On Thu, Apr 17, 2014 at 7:58 PM, Joel Armstrong notifications@github.comwrote:

Sorry, I think the attachment didn't work since it got sent by email to github. Could you send it to jcarmstr@ucsc.edu, or paste it in the github issue?

Thanks!

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40778530 .

leirhyh commented 10 years ago

Hi Joel: Today, I re-installed progressiveCactus and use make ucsc. I've got the following errors: In file included from ../../phast/include/trees.h:24:0, from ../../phast/include/tree_model.h:26, from inc/halPhyloP.h:16, from impl/halPhyloPMain.cpp:13: ../../phast/include/lists.h: In function ‘void lst_arrset(List, int, void_)’: ../../phast/include/lists.h:75:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] /usr/bin/ld: cannot find -lphast /usr/bin/ld: cannot find -ltmg /usr/bin/ld: cannot find -lblaswr /usr/bin/ld: cannot find -lf2c collect2: ld returned 1 exit status make[3]: * [../bin//halPhyloP] Error 1 make[3]: Leaving directory /software/progressiveCactus/submodules/hal/phyloP' make[2]: *** [all.phyloP] Error 2 make[2]: Leaving directory/software/progressiveCactus/submodules/hal' make[1]: *\ [ucsc.hal] Error 2 make[1]: Leaving directory `/software/progressiveCactus/submodules' make: * [ucsc] Error 2

What do you think?

Thanks,

All the best,

Runhua

On Tue, Apr 22, 2014 at 8:59 AM, Runhua Lei runhua.lei@gmail.com wrote:

Hi, Joel: Please see the cactus.log as follows. Thanks, Runhua

2014-04-16 12:22:38.325192: Beginning Progressive Cactus Alignment Got message from job at time: 1397668959.47 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mar55.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mar55.fa Total-sequences: 134774 Total-length: 21412782 Proportion-repeat-masked: 0.000308 ProportionNs: 0.000308 N50: 0 Median-sequence-length: 144 Got message from job at time: 1397668960.16 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/rano217.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/rano217.fa Total-sequences: 229100 Total-length: 41765894 Proportion-repeat-masked: 0.000220 ProportionNs: 0.000220 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397668960.2 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/bema8.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/bema8.fa Total-sequences: 237877 Total-length: 44125254 Proportion-repeat-masked: 0.000207 ProportionNs: 0.000207 N50: 0 Median-sequence-length: 156 Got message from job at time: 1397668960.36 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/nofy610.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/nofy610.fa Total-sequences: 272528 Total-length: 51925339 Proportion-repeat-masked: 0.000177 ProportionNs: 0.000177 N50: 0 Median-sequence-length: 153 Got message from job at time: 1397668961.17 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/dasi523.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/dasi523.fa Total-sequences: 155896 Total-length: 25711621 Proportion-repeat-masked: 0.000286 ProportionNs: 0.000286 N50: 0 Median-sequence-length: 147 Got message from job at time: 1397668961.21 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/tafo69.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/tafo69.fa Total-sequences: 277313 Total-length: 49938213 Proportion-repeat-masked: 0.000143 ProportionNs: 0.000143 N50: 0 Median-sequence-length: 142 Got message from job at time: 1397668961.54 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mas66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/mas66.fa Total-sequences: 221282 Total-length: 40013045 Proportion-repeat-masked: 0.000232 ProportionNs: 0.000232 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397668962.08 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/fan66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/fan66.fa Total-sequences: 277502 Total-length: 52675079 Proportion-repeat-masked: 0.000166 ProportionNs: 0.000166 N50: 0 Median-sequence-length: 150 Got message from job at time: 1397668962.25 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/m155.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/m155.fa Total-sequences: 115604 Total-length: 18319508 Proportion-repeat-masked: 0.000285 ProportionNs: 0.000285 N50: 0 Median-sequence-length: 143 Got message from job at time: 1397668962.99 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/and34.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/and34.fa Total-sequences: 285209 Total-length: 54341263 Proportion-repeat-masked: 0.000165 ProportionNs: 0.000165 N50: 0 Median-sequence-length: 149 Got message from job at time: 1397668963.11 : Before running any preprocessing on the assembly: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/ranol61.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /software/progressiveCactus/submodules/cactusTestData/evolver/primates/lemur/ranol61.fa Total-sequences: 328828 Total-length: 58321330 Proportion-repeat-masked: 0.000136 ProportionNs: 0.000136 N50: 0 Median-sequence-length: 128 Got message from job at time: 1397669384.56 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_mar55.fa Total-sequences: 134774 Total-length: 21412782 Proportion-repeat-masked: 0.003630 ProportionNs: 0.000308 N50: 0 Median-sequence-length: 144 Got message from job at time: 1397669448.03 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_rano217.fa Total-sequences: 229100 Total-length: 41765894 Proportion-repeat-masked: 0.005052 ProportionNs: 0.000220 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397669451.07 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_bema8.fa Total-sequences: 237877 Total-length: 44125254 Proportion-repeat-masked: 0.005676 ProportionNs: 0.000207 N50: 0 Median-sequence-length: 156 Got message from job at time: 1397669452.88 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_dasi523.fa Total-sequences: 155896 Total-length: 25711621 Proportion-repeat-masked: 0.004171 ProportionNs: 0.000286 N50: 0 Median-sequence-length: 147 Got message from job at time: 1397669455.23 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_nofy610.fa Total-sequences: 272528 Total-length: 51925339 Proportion-repeat-masked: 0.006137 ProportionNs: 0.000177 N50: 0 Median-sequence-length: 153 Got message from job at time: 1397669455.23 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_m155.fa Total-sequences: 115604 Total-length: 18319508 Proportion-repeat-masked: 0.005549 ProportionNs: 0.000285 N50: 0 Median-sequence-length: 143 Got message from job at time: 1397669457.93 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_mas66.fa Total-sequences: 221282 Total-length: 40013045 Proportion-repeat-masked: 0.005201 ProportionNs: 0.000232 N50: 0 Median-sequence-length: 155 Got message from job at time: 1397669458.59 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_tafo69.fa Total-sequences: 277313 Total-length: 49938213 Proportion-repeat-masked: 0.005126 ProportionNs: 0.000143 N50: 0 Median-sequence-length: 142 Got message from job at time: 1397669458.88 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_and34.fa Total-sequences: 285209 Total-length: 54341263 Proportion-repeat-masked: 0.006265 ProportionNs: 0.000164 N50: 0 Median-sequence-length: 149 Got message from job at time: 1397669459.05 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_fan66.fa Total-sequences: 277502 Total-length: 52675079 Proportion-repeat-masked: 0.006250 ProportionNs: 0.000166 N50: 0 Median-sequence-length: 150 Got message from job at time: 1397669462.75 : After preprocessing assembly we got the following stats: Input-sample: ./lemur/sequenceData/_software_progressiveCactus_submodules_cactusTestData_evolver_primates_lemur_ranol61.fa Total-sequences: 328828 Total-length: 58321330 Proportion-repeat-masked: 0.006059 ProportionNs: 0.000136 N50: 0 Median-sequence-length: 128 Got message from job at time: 1397669463.27 : The longest path in the tree is 0.385017 Got message from job at time: 1397669463.27 : Made argument lastzArguments=--step=1 --ambiguous=iupac,100 --ydrop=3000 in tag caf with divergence threshold of 9223372036854775807 for longest path of 0.38501709 (useDefaultDivergences=False) The job seems to have left a log file, indicating failure: /software/progressiveCactus/lemur/jobTree/jobs/t0/job Reporting file: /software/progressiveCactus/lemur/jobTree/jobs/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/software/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/software/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/software/progressiveCactus/submodules/cactus/pipeline/ktserverJobTree.py", line 139, in run log.txt: killPingInterval=self.runTimestep) log.txt: File "/software/progressiveCactus/submodules/cactus/pipeline/ktserverControl.py", line 130, in runKtserver log.txt: raise e log.txt: RuntimeError: Unable to launch ktserver. Server log is: /software/progressiveCactus/lemur/progressiveAlignment/Anc09/Anc09/Anc09_DB/ktout.log log.txt: Exiting the slave because of a failed job on host genetics2 log.txt: Due to failure we are reducing the remaining retry count of job /software/progressiveCactus/lemur/jobTree/jobs/t0/job to 0 log.txt: We have set the default memory of the failed job to 34359738368 bytes Job: /software/progressiveCactus/lemur/jobTree/jobs/t0/job is completely failed

On Thu, Apr 17, 2014 at 7:58 PM, Joel Armstrong notifications@github.comwrote:

Sorry, I think the attachment didn't work since it got sent by email to github. Could you send it to jcarmstr@ucsc.edu, or paste it in the github issue?

Thanks!

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18?utm_campaign=website&utm_source=sendgrid.com&utm_medium=email#issuecomment-40778530 .

leirhyh commented 10 years ago

Hi, Joel and Glenn: There was a post about the similar issues about *RuntimeError: Unable to launch ktserver" As you suggested, your update version can solve this issue. It looks that there may be still issue in my case. Any advice and suggestions?

Thanks,

All the best,

Runhua

joelarmstrong commented 10 years ago

Hi Runhua,

Really sorry about the delay!

I'm a little stumped about the ktserver error you're seeing. This could be caused by all the ports in the region 1978-2078 already being taken, or the ktserver crashing when run. I think the problem is most likely with the ktserver install. Maybe recompiling the entire package with "make clean" then "make" will help, but first, to fix the compiler error:

The compiler error that you saw when you ran "make ucsc" might mean that phyloP wasn't enabled at first, but then got enabled somehow. If you run "ENABLE_PHYLOP=1 make" hopefully the compiler error will be fixed.

leirhyh commented 10 years ago

Hi, Joel: I did install the ProgressiveCactus in my dell computer with Ubuntu 12.04. I run successfully a data set with 21 taxon. Today, I run a dataset with 30 taxa and have the following errors: genetics@genetics:~/genomealn$ /software/progressiveCactus/bin/runProgressiveCactus.sh /home/genetics/genomealn/lemurtotal.txt /home/genetics/genomealn/lemurtotal /home/genetics/genomealn/lemurtotal/lemurtotal.hal

Beginning Alignment Beginning HAL Export There are 1 active jobs, 1 parent jobs with children, 1 totally failed jobs and 29 empty jobs (i.e. finished but not cleaned up) currently in job tree: /home/genetics/genomealn/lemurtotal/jobTree Error: Command: . /software/progressiveCactus/bin/../src/../environment && cactus2hal.py /home/genetics/genomealn/lemurtotal/progressiveAlignment/progressiveAlignment_project.xml /home/genetics/genomealn/lemurtotal/lemurtotal.hal >> /home/genetics/genomealn/lemurtotal/cactus.log 2>&1 exited with non-zero status 1

Temporary data was left in: /home/genetics/genomealn/lemurtotal More information can be found in /home/genetics/genomealn/lemurtotal/cactus.log

Please see the cactus.log in attachment. Could you please help me solve this issue?

Thanks,

Runhua

On Fri, Apr 25, 2014 at 4:24 PM, Joel Armstrong notifications@github.comwrote:

Hi Runhua,

Really sorry about the delay!

I'm a little stumped about the ktserver error you're seeing. This could be caused by all the ports in the region 1978-2078 already being taken, or the ktserver crashing when run. I think the problem is most likely with the ktserver install. Maybe recompiling the entire package with "make clean" then "make" will help, but first, to fix the compiler error:

The compiler error that you saw when you ran "make ucsc" might mean that phyloP wasn't enabled at first, but then got enabled somehow. If you run "ENABLE_PHYLOP=1 make" hopefully the compiler error will be fixed.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-41440986 .

joelarmstrong commented 10 years ago

Hi Runhua,

This looks like an issue with headers in the human fasta file not being unique.

Technically speaking, only the first space-separated word in a FASTA header is the sequence identifier. Since some of the tools we use only the first word, that word needs to be unique within a genome.

So when a fasta header looks like: hg19_refGene_NM_001271887_0 range=chr1:121107052-121107316 5'pad=100 3'pad=100 strand=+ repeatMasking=none

I assume there are other sequences with different ranges but the same first word, "hg19_refGene_NM_001271887_0". It may work to replace all spaces with | characters in the fasta headers--that's what I'd try first, at least.

leirhyh commented 10 years ago

Hi, Joel: I will check and screen the sequence first and run it again. I will let you know if I made some progress. Thanks and I appreciate your time. All the best,

Runhua

On Thu, May 22, 2014 at 4:52 PM, Joel Armstrong notifications@github.comwrote:

Hi Runhua,

This looks like an issue with headers in the human fasta file not being unique.

Technically speaking, only the first space-separated word in a FASTA header is the sequence identifier. Since some of the tools we use only the first word, that word needs to be unique within a genome.

So when a fasta header looks like: hg19_refGene_NM_001271887_0 range=chr1:121107052-121107316 5'pad=100 3'pad=100 strand=+ repeatMasking=none

I assume there are other sequences with different ranges but the same first word, "hg19_refGene_NM_001271887_0". It may work to replace all spaces with | characters in the fasta headers--that's what I'd try first, at least.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-43948822 .

benedictpaten commented 10 years ago

Hey Joel, Did it not warn about the sequence headers during the setup phase?, or is Ru hua using a version without this feature?, if the latter we should make sure it's pushed to the appropriate (master?) branch

Benedict (from phone) On May 22, 2014 2:52 PM, "Joel Armstrong" notifications@github.com wrote:

Hi Runhua,

This looks like an issue with headers in the human fasta file not being unique.

Technically speaking, only the first space-separated word in a FASTA header is the sequence identifier. Since some of the tools we use only the first word, that word needs to be unique within a genome.

So when a fasta header looks like: hg19_refGene_NM_001271887_0 range=chr1:121107052-121107316 5'pad=100 3'pad=100 strand=+ repeatMasking=none

I assume there are other sequences with different ranges but the same first word, "hg19_refGene_NM_001271887_0". It may work to replace all spaces with | characters in the fasta headers--that's what I'd try first, at least.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-43948822 .

leirhyh commented 10 years ago

Hi, Joel: As you said, I changed the human reference and add contig number to each header and works now. Thanks and I appreciate your time. All the best,

Runhua

On Sun, May 25, 2014 at 7:26 PM, Benedict Paten notifications@github.comwrote:

Hey Joel, Did it not warn about the sequence headers during the setup phase?, or is Ru hua using a version without this feature?, if the latter we should make sure it's pushed to the appropriate (master?) branch

Benedict (from phone) On May 22, 2014 2:52 PM, "Joel Armstrong" notifications@github.com wrote:

Hi Runhua,

This looks like an issue with headers in the human fasta file not being unique.

Technically speaking, only the first space-separated word in a FASTA header is the sequence identifier. Since some of the tools we use only the first word, that word needs to be unique within a genome.

So when a fasta header looks like: hg19_refGene_NM_001271887_0 range=chr1:121107052-121107316 5'pad=100 3'pad=100 strand=+ repeatMasking=none

I assume there are other sequences with different ranges but the same first word, "hg19_refGene_NM_001271887_0". It may work to replace all spaces with | characters in the fasta headers--that's what I'd try first, at least.

— Reply to this email directly or view it on GitHub< https://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-43948822>

.

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/18#issuecomment-44149854 .

joelarmstrong commented 10 years ago

Great to hear Runhua. Let me know if there are any more problems.

Benedict, it did warn during the setup phase, but didn't fail out completely. It does fail completely when I try it, but maybe it is something weird when rerunning the script. Or maybe progressiveCactus isn't pointing at the right commit. I'll try with a fresh version sometime tonight.

leirhyh commented 10 years ago

Hi, Joel: A week ago, I run a big data set with progressiveCactus which is OK. However, when I run a small data set today, I got errors as below. Could you please help me fix this issue? Thanks and I appreciate your time.

All the best,

Runhua

2014-06-30 16:11:36.133725: Beginning Progressive Cactus Alignment

Got message from job at time: 1404162696.9 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/TVY795.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/TVY795.fa Total-sequences: 10710 Total-length: 1992360 Proportion-repeat-masked: 0.000100 ProportionNs: 0.000100 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162696.9 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/ZAH272.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/ZAH272.fa Total-sequences: 9187 Total-length: 1606494 Proportion-repeat-masked: 0.000323 ProportionNs: 0.000323 N50: 0 Median-sequence-length: 154 Got message from job at time: 1404162696.91 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/MAS66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/MAS66.fa Total-sequences: 10754 Total-length: 2013658 Proportion-repeat-masked: 0.000212 ProportionNs: 0.000212 N50: 0 Median-sequence-length: 160 Got message from job at time: 1404162696.91 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/DASI523.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/DASI523.fa Total-sequences: 7660 Total-length: 1299020 Proportion-repeat-masked: 0.000311 ProportionNs: 0.000311 N50: 0 Median-sequence-length: 151 Got message from job at time: 1404162696.92 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/KIBO22.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/KIBO22.fa Total-sequences: 10868 Total-length: 2037476 Proportion-repeat-masked: 0.000089 ProportionNs: 0.000089 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162696.93 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/AND34.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/AND34.fa Total-sequences: 13107 Total-length: 2616770 Proportion-repeat-masked: 0.000191 ProportionNs: 0.000191 N50: 0 Median-sequence-length: 158 Got message from job at time: 1404162696.93 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/RANOL61.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/RANOL61.fa Total-sequences: 13333 Total-length: 2581795 Proportion-repeat-masked: 0.000105 ProportionNs: 0.000105 N50: 0 Median-sequence-length: 149 Got message from job at time: 1404162696.93 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/WEST1.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/WEST1.fa Total-sequences: 11799 Total-length: 2353845 Proportion-repeat-masked: 0.000012 ProportionNs: 0.000012 N50: 0 Median-sequence-length: 166 Got message from job at time: 1404162696.95 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/FAN66.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/FAN66.fa Total-sequences: 12921 Total-length: 2560824 Proportion-repeat-masked: 0.000119 ProportionNs: 0.000119 N50: 0 Median-sequence-length: 158 Got message from job at time: 1404162696.95 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/KIAN84.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/KIAN84.fa Total-sequences: 13998 Total-length: 2742816 Proportion-repeat-masked: 0.000313 ProportionNs: 0.000313 N50: 0 Median-sequence-length: 148 Got message from job at time: 1404162696.95 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/M155.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/M155.fa Total-sequences: 6247 Total-length: 1010713 Proportion-repeat-masked: 0.000353 ProportionNs: 0.000353 N50: 0 Median-sequence-length: 147 Got message from job at time: 1404162696.95 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/MAR55.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/MAR55.fa Total-sequences: 6786 Total-length: 1098162 Proportion-repeat-masked: 0.000306 ProportionNs: 0.000306 N50: 0 Median-sequence-length: 146 Got message from job at time: 1404162696.98 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/BEMA8.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/BEMA8.fa Total-sequences: 11338 Total-length: 2178048 Proportion-repeat-masked: 0.000198 ProportionNs: 0.000198 N50: 1 Median-sequence-length: 162 Got message from job at time: 1404162696.98 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/FIA528.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/FIA528.fa Total-sequences: 4970 Total-length: 762863 Proportion-repeat-masked: 0.000147 ProportionNs: 0.000147 N50: 0 Median-sequence-length: 144 Got message from job at time: 1404162697.03 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/TAFO69.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/TAFO69.fa Total-sequences: 11909 Total-length: 2264620 Proportion-repeat-masked: 0.000141 ProportionNs: 0.000141 N50: 0 Median-sequence-length: 154 Got message from job at time: 1404162697.03 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/MERY3.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/MERY3.fa Total-sequences: 3067 Total-length: 454861 Proportion-repeat-masked: 0.000306 ProportionNs: 0.000306 N50: 0 Median-sequence-length: 139 Got message from job at time: 1404162697.03 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/HIH19.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/HIH19.fa Total-sequences: 13392 Total-length: 2589409 Proportion-repeat-masked: 0.000115 ProportionNs: 0.000115 N50: 0 Median-sequence-length: 147 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/KIR618.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/KIR618.fa Total-sequences: 12027 Total-length: 2389612 Proportion-repeat-masked: 0.000004 ProportionNs: 0.000004 N50: 0 Median-sequence-length: 165 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/NOFY610.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/NOFY610.fa Total-sequences: 12750 Total-length: 2530915 Proportion-repeat-masked: 0.000183 ProportionNs: 0.000183 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/RANO217.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/RANO217.fa Total-sequences: 10868 Total-length: 2050701 Proportion-repeat-masked: 0.000264 ProportionNs: 0.000264 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/JAM47.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/JAM47.fa Total-sequences: 11712 Total-length: 2289845 Proportion-repeat-masked: 0.000228 ProportionNs: 0.000228 N50: 0 Median-sequence-length: 162 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/BEMA23.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/BEMA23.fa Total-sequences: 12788 Total-length: 2468613 Proportion-repeat-masked: 0.000188 ProportionNs: 0.000188 N50: 0 Median-sequence-length: 150 Got message from job at time: 1404162697.12 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/JAR37.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/JAR37.fa Total-sequences: 12614 Total-length: 2412791 Proportion-repeat-masked: 0.000132 ProportionNs: 0.000132 N50: 0 Median-sequence-length: 151 Got message from job at time: 1404162697.14 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/PJX022.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/PJX022.fa Total-sequences: 12848 Total-length: 3036431 Proportion-repeat-masked: 0.000294 ProportionNs: 0.000294 N50: 0 Median-sequence-length: 183 Got message from job at time: 1404162697.14 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/PJX023.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/PJX023.fa Total-sequences: 13096 Total-length: 3078408 Proportion-repeat-masked: 0.000301 ProportionNs: 0.000301 N50: 0 Median-sequence-length: 180 Got message from job at time: 1404162697.15 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/Otolemur.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/Otolemur.fa Total-sequences: 8963 Total-length: 1548903 Proportion-repeat-masked: 0.000233 ProportionNs: 0.000233 N50: 0 Median-sequence-length: 150 Got message from job at time: 1404162697.15 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/4776.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/4776.fa Total-sequences: 9677 Total-length: 1745342 Proportion-repeat-masked: 0.000278 ProportionNs: 0.000278 N50: 0 Median-sequence-length: 156 Got message from job at time: 1404162697.19 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/7128.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/7128.fa Total-sequences: 8653 Total-length: 1481661 Proportion-repeat-masked: 0.000371 ProportionNs: 0.000371 N50: 0 Median-sequence-length: 153 Got message from job at time: 1404162697.23 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/6139.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/6139.fa Total-sequences: 10735 Total-length: 2003950 Proportion-repeat-masked: 0.000135 ProportionNs: 0.000135 N50: 0 Median-sequence-length: 160 Got message from job at time: 1404162697.32 : Before running any preprocessing on the assembly: /home/genetics/genomealn/data/chr5/Human.fa got following stats (assembly may be listed as temp file if input sequences from a directory): Input-sample: /home/genetics/genomealn/data/chr5/Human.fa Total-sequences: 16928 Total-length: 6823945 Proportion-repeat-masked: 0.496129 ProportionNs: 0.000000 N50: 200 Median-sequence-length: 328 Got message from job at time: 1404162707.91 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_DASI523.fa Total-sequences: 7660 Total-length: 1299020 Proportion-repeat-masked: 0.000691 ProportionNs: 0.000311 N50: 0 Median-sequence-length: 151 Got message from job at time: 1404162711.14 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_ZAH272.fa Total-sequences: 9187 Total-length: 1606494 Proportion-repeat-masked: 0.000495 ProportionNs: 0.000323 N50: 0 Median-sequence-length: 154 Got message from job at time: 1404162716.08 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_TVY795.fa Total-sequences: 10710 Total-length: 1992360 Proportion-repeat-masked: 0.001474 ProportionNs: 0.000100 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162716.19 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_MAS66.fa Total-sequences: 10754 Total-length: 2013658 Proportion-repeat-masked: 0.000883 ProportionNs: 0.000212 N50: 0 Median-sequence-length: 160 Got message from job at time: 1404162716.31 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_M155.fa Total-sequences: 6247 Total-length: 1010713 Proportion-repeat-masked: 0.000402 ProportionNs: 0.000353 N50: 0 Median-sequence-length: 147 Got message from job at time: 1404162717.34 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_KIBO22.fa Total-sequences: 10868 Total-length: 2037476 Proportion-repeat-masked: 0.001261 ProportionNs: 0.000089 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162720.13 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_MAR55.fa Total-sequences: 6786 Total-length: 1098162 Proportion-repeat-masked: 0.000306 ProportionNs: 0.000306 N50: 0 Median-sequence-length: 146 Got message from job at time: 1404162720.38 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_WEST1.fa Total-sequences: 11799 Total-length: 2353845 Proportion-repeat-masked: 0.001844 ProportionNs: 0.000012 N50: 0 Median-sequence-length: 166 Got message from job at time: 1404162720.83 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_MERY3.fa Total-sequences: 3067 Total-length: 454861 Proportion-repeat-masked: 0.000306 ProportionNs: 0.000306 N50: 0 Median-sequence-length: 139 Got message from job at time: 1404162721.7 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_FIA528.fa Total-sequences: 4970 Total-length: 762863 Proportion-repeat-masked: 0.000147 ProportionNs: 0.000147 N50: 0 Median-sequence-length: 144 Got message from job at time: 1404162722.25 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_RANOL61.fa Total-sequences: 13333 Total-length: 2581795 Proportion-repeat-masked: 0.001478 ProportionNs: 0.000105 N50: 0 Median-sequence-length: 149 Got message from job at time: 1404162722.45 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_FAN66.fa Total-sequences: 12921 Total-length: 2560824 Proportion-repeat-masked: 0.001696 ProportionNs: 0.000119 N50: 0 Median-sequence-length: 158 Got message from job at time: 1404162723.77 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_AND34.fa Total-sequences: 13107 Total-length: 2616770 Proportion-repeat-masked: 0.001843 ProportionNs: 0.000191 N50: 0 Median-sequence-length: 158 Got message from job at time: 1404162724.0 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_KIAN84.fa Total-sequences: 13998 Total-length: 2742816 Proportion-repeat-masked: 0.002737 ProportionNs: 0.000313 N50: 0 Median-sequence-length: 148 Got message from job at time: 1404162737.21 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_BEMA8.fa Total-sequences: 11338 Total-length: 2178048 Proportion-repeat-masked: 0.001334 ProportionNs: 0.000198 N50: 1 Median-sequence-length: 162 Got message from job at time: 1404162737.63 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_TAFO69.fa Total-sequences: 11909 Total-length: 2264620 Proportion-repeat-masked: 0.000938 ProportionNs: 0.000141 N50: 0 Median-sequence-length: 154 Got message from job at time: 1404162742.0 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_RANO217.fa Total-sequences: 10868 Total-length: 2050701 Proportion-repeat-masked: 0.001285 ProportionNs: 0.000264 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162744.8 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_HIH19.fa Total-sequences: 13392 Total-length: 2589409 Proportion-repeat-masked: 0.001524 ProportionNs: 0.000115 N50: 0 Median-sequence-length: 147 The job seems to have left a log file, indicating failure: /home/genetics/genomealn/lemurchr5/jobTree/jobs/t3/t3/t0/job Reporting file: /home/genetics/genomealn/lemurchr5/jobTree/jobs/t3/t3/t0/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/software/progressiveCactus/submodules/cactus/bin/cactus_checkUniqueHeaders.py", line 56, in log.txt: exit(main()) log.txt: File "/software/progressiveCactus/submodules/cactus/bin/cactus_checkUniqueHeaders.py", line 50, in main log.txt: raise RuntimeError("We found a duplicated fasta header: %s" % header) log.txt: RuntimeError: We found a duplicated fasta header: chr5_58511503_58511894 log.txt: Traceback (most recent call last): log.txt: File "/software/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/software/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/software/progressiveCactus/submodules/cactus/preprocessor/cactus_preprocessor.py", line 59, in run log.txt: popenPush(cmdline, " ".join(self.seqPaths)) log.txt: File "/software/progressiveCactus/submodules/sonLib/bioio.py", line 221, in popenPush log.txt: raise RuntimeError("Command: %s with stdin string '%s' exited with non-zero status %i" % (command, stdinString, sts)) log.txt: RuntimeError: Command: cactus_checkUniqueHeaders.py --checkUCSC "/home/genetics/genomealn/data/chr5/Human.fa" with stdin string '/home/genetics/genomealn/data/chr5/Human.fa' exited with non-zero status 1 log.txt: Exiting the slave because of a failed job on host genetics log.txt: Due to failure we are reducing the remaining retry count of job /home/genetics/genomealn/lemurchr5/jobTree/jobs/t3/t3/t0/job to 0 log.txt: We have set the default memory of the failed job to 8589934592 bytes Job: /home/genetics/genomealn/lemurchr5/jobTree/jobs/t3/t3/t0/job is completely failed Got message from job at time: 1404162745.32 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_JAM47.fa Total-sequences: 11712 Total-length: 2289845 Proportion-repeat-masked: 0.001355 ProportionNs: 0.000228 N50: 0 Median-sequence-length: 162 Got message from job at time: 1404162745.44 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_KIR618.fa Total-sequences: 12027 Total-length: 2389612 Proportion-repeat-masked: 0.001114 ProportionNs: 0.000004 N50: 0 Median-sequence-length: 165 Got message from job at time: 1404162746.03 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_NOFY610.fa Total-sequences: 12750 Total-length: 2530915 Proportion-repeat-masked: 0.002677 ProportionNs: 0.000183 N50: 0 Median-sequence-length: 161 Got message from job at time: 1404162746.75 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_BEMA23.fa Total-sequences: 12788 Total-length: 2468613 Proportion-repeat-masked: 0.001515 ProportionNs: 0.000188 N50: 0 Median-sequence-length: 150 Got message from job at time: 1404162746.98 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_Otolemur.fa Total-sequences: 8963 Total-length: 1548903 Proportion-repeat-masked: 0.001346 ProportionNs: 0.000233 N50: 0 Median-sequence-length: 150 Got message from job at time: 1404162748.09 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_JAR37.fa Total-sequences: 12614 Total-length: 2412791 Proportion-repeat-masked: 0.001307 ProportionNs: 0.000132 N50: 0 Median-sequence-length: 151 Got message from job at time: 1404162749.86 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_7128.fa Total-sequences: 8653 Total-length: 1481661 Proportion-repeat-masked: 0.000451 ProportionNs: 0.000371 N50: 0 Median-sequence-length: 153 Got message from job at time: 1404162752.05 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_4776.fa Total-sequences: 9677 Total-length: 1745342 Proportion-repeat-masked: 0.000565 ProportionNs: 0.000278 N50: 0 Median-sequence-length: 156 Got message from job at time: 1404162758.45 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_6139.fa Total-sequences: 10735 Total-length: 2003950 Proportion-repeat-masked: 0.000998 ProportionNs: 0.000135 N50: 0 Median-sequence-length: 160 Got message from job at time: 1404162766.01 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_PJX022.fa Total-sequences: 12848 Total-length: 3036431 Proportion-repeat-masked: 0.003573 ProportionNs: 0.000294 N50: 0 Median-sequence-length: 183 Got message from job at time: 1404162766.18 : After preprocessing assembly we got the following stats: Input-sample: /home/genetics/genomealn/lemurchr5/sequenceData/_home_genetics_genomealn_data_chr5_PJX023.fa Total-sequences: 13096 Total-length: 3078408 Proportion-repeat-masked: 0.003384 ProportionNs: 0.000301 N50: 0 Median-sequence-length: 180

2014-06-30 16:12:46.216500: Finished Progressive Cactus Alignment

2014-06-30 16:12:46.221891: Beginning HAL Export

hal exception caught: Error opening/home/genetics/genomealn/lemurchr5/progressiveAlignment/Anc00/Anc00_hal.c2h Command exited with non-zero status 1 0.00user 0.00system 0:00.09elapsed 6%CPU (0avgtext+0avgdata 10832maxresident)k 5792inputs+0outputs (21major+721minor)pagefaults 0swaps rm -f /home/genetics/genomealn/lemurchr5/lemurchr5.hal time halAppendCactusSubtree '/home/genetics/genomealn/lemurchr5/progressiveAlignment/Anc00/Anc00_hal.c2h' '/home/genetics/genomealn/lemurchr5/progressiveAlignment/Anc00/Anc00_hal.fa' '(Anc01:0.994168175,Human:0.994168175)Anc00;' '/home/genetics/genomealn/lemurchr5/lemurchr5.hal' Traceback (most recent call last): File "/software/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 122, in main(); File "/software/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 113, in main system(cmdline) File "/software/progressiveCactus/submodules/sonLib/bioio.py", line 182, in system raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts)) RuntimeError: Command: time halAppendCactusSubtree '/home/genetics/genomealn/lemurchr5/progressiveAlignment/Anc00/Anc00_hal.c2h' '/home/genetics/genomealn/lemurchr5/progressiveAlignment/Anc00/Anc00_hal.fa' '(Anc01:0.994168175,Human:0.994168175)Anc00;' '/home/genetics/genomealn/lemurchr5/lemurchr5.hal' exited with non-zero status 1

On Thu, Apr 17, 2014 at 2:15 PM, Joel Armstrong notifications@github.com wrote:

Reopened #18 https://github.com/glennhickey/progressiveCactus/issues/18.

— Reply to this email directly or view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/18.

joelarmstrong commented 10 years ago

Hi Runhua,

Looks like there are two sequences with the ID chr5_58511503_58511894 in Human.fa. The first word (space-separated) in every sequence header must be unique within its genome. Once the headers are unique the alignment should run fine.

Hopefully this helps!

Thanks -Joel