I am still having problems with log files. The symptoms are: 1. The log file is very short - my most recent one ( https://www.synapse.org/#!Synapse:syn10843630 ) is 601 bytes 2. The place where the log is truncated seems arbitrary. It stops in a shell script with one 'echo' statement, but does not give the next, even though it is just an echo statement 3. It says that the submission has 'run successfully' - but I put 'exit 42' at the bottom of the script, which should give an error ending. So it seems that it does not get to the bottom of the script, even though it says 'Your submission "Made sure the latest version of 'find' is available in case that's the problem - and added exit 42" (ID: 9636177) to the MM_Challenge_1_Express_Lane has run successfully'. Does the script that runs 'score_sc1.sh' check for an error exit? 4. I have tried a number of base models for docker, but I get the same symptoms, so it doesn't seem that that is the problem. I am using 'FROM ubuntu:zesty' in Dockerfile, as well as having 'apt-get -y upgrade ; apt-get update' to make sure everything is at the latest version. I have also manually installed 'coreutils' and 'findutils' in case (unlikely, I know, but I have been troubleshooting) basic utilities were missing from the minimal version of Ubuntu. 5. I thought it might be a problem with the setting of the environment variable, but even giving fully qualified names ( like '/usr/bin/find' ) gives the same result. 6. The system information from the machine it is running on is: ``` System information: Linux b6b00e274607 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ``` 7. In case it was a resource problem, I ran '/usr/bin/vmstat --timestamp --unit=M ', the output looks fine: ``` procs -----------memory---------- ---swap-- -----io---- -system-- ------cpu----- -----timestamp----- r b swpd free buff cache si so bi bo in cs us sy id wa st UTC 2 0 0 30091 1461 31646 0 0 6 46 2 0 3 1 96 0 0 2017-09-19 09:51:32 ``` There should be no problem on a machine with 30Gb of memory! I'd be very grateful for any suggestions of how to fix this.

Created by Peter Brooks fustbariclation
Thank you for the update, Tom. I am still having the problems with truncation of the log file. I am trying various things to see if I can change it, but it seems persistent. It is particularly odd that it happens when only simple bash commands are executing, nothing complicated. I have even tried changing the OS version from Zesty to Xenial, but the problem persists.
Dear Peter, 1. I do see that your log file was cut off. That is indeed very strange and I will look into that issue. It could be that your docker container threw a silent error and the logs did not catch it. 2. It is rather arbitrary as every minute the log file gets updated. Unless in a minutes time your log file went over the 50 kb size limit, there should be no reason your log file isn't returned. 3. Exit 42 does not cause an error in the shell script. When you put exit 42 on the bottom of a shell script lets say for example a shell script called `temp.sh` ``` echo "temp" exit 42 ``` When you run this shell script `bash temp.sh`, it is able to run all the way through without having an error message. This could be the reason why docker says that your submission is running successfully. Apologies for the issues that you are having. We are updating the data and infrastructure to deal with certain issues. Thanks for your participation. Best, Tom
I think that the e-mail that has just arrived from Michael Mason could be the problem. My script was working, but now has the above problems. It might be because the files are now bgzipped, when they were not before. I am using awk to read the .vcf files, so I'll have to decompress them, and then see if the script starts working again.

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