benedictpaten
commented
9 years ago Sorry for the hassle. I pushed a v0.1 release last night. Can you confirm you are using this (i.e. that you've updated your distribution according to the instructions on the website / checked-out a fresh distribution)? Also, are you using the virtual-env?
On Mon, Apr 20, 2015 at 10:54 AM, twaddlac notifications@github.com wrote:
Good day,
I am receiving an error when trying to run marginAlign with the default parameters. Below the command that I ran as well as the error report. Please let me know if you need any other information, thank you very much!
alan@zoidberg:~/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in$ /opt/bioinformatics-software/minion-software/margin/marginAlign first-run.passed.fastq ../../lamda-phage.fasta first.passed.sam Got message from job at time: 1429552015.62 : Going to chain sam file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/gTD0/tmp_4vbY30VFrP/temp.sam Got message from job at time: 1429552015.62 : Going to realign sam file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/gTD1/tmp_pxHowcXufF/temp.sam to create output sam file: first.passed.sam with match gamma 0.5 and gap gamma 0.0 and model /opt/bioinformatics-software/minion-software/margin/src/margin/mappers/last_hmm20.txt The job seems to have left a log file, indicating failure: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job Reporting file: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/opt/bioinformatics-software/minion-software/margin/submodules/jobTree/scriptTree/target.py", line 197, in run log.txt: func(((self,) + tuple(self.args)), *_self.kwargs) log.txt: File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlignLib.py", line 345, in realignSamFile3TargetFn log.txt: ops += map(lambda op : (op.type, op.length), pA.operationList) log.txt: AttributeError: 'NoneType' object has no attribute 'operationList' log.txt: Exiting the slave because of a failed job on host zoidberg log.txt: Due to failure we are reducing the remaining retry count of job /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /home/alan/projects/minion/lambda-burn-in/filtered-data/lambda-burn-in/jobTree/jobs/job is completely failed Traceback (most recent call last): File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlign.py", line 91, in
main() File "/opt/bioinformatics-software/minion-software/margin/src/margin/marginAlign.py", line 87, in main raise RuntimeError("Got failed jobs") RuntimeError: Got failed jobs — Reply to this email directly or view it on GitHub https://github.com/benedictpaten/marginAlign/issues/18.
twaddlac
Good day,
I am receiving an error when trying to run marginAlign with the default parameters. Below the command that I ran as well as the error report. Please let me know if you need any other information, thank you very much!