contributors:team_4_page
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contributors:team_4_page [2015/05/11 09:01] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/20 18:49] sihussai |
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| The success of this run means we are probably ready to do a run with all the data (not including the mate-pair data, that can be used for scaffolding later). For that run, the different trimmed files for each library should be concatenated, so that the run involves only the actual number of libraries we had (I believe 4?). It should also use many more than 10 processes. | The success of this run means we are probably ready to do a run with all the data (not including the mate-pair data, that can be used for scaffolding later). For that run, the different trimmed files for each library should be concatenated, so that the run involves only the actual number of libraries we had (I believe 4?). It should also use many more than 10 processes. | ||
| + | |||
| + | =====Test with more data===== | ||
| + | This run was also done using version 1.5.2. I used SGE job arrays to submit multiple assemblies with different k values, k=55-65 and 27-37, odds only. (Using this many similar ks is probably unnecessary.) The syntax for submitting an array w/ multiple ks is | ||
| + | |||
| + | qsub -t 55-65:2 slug-pe.sh | ||
| + | | ||
| + | where slug-pe.sh uses $SGE_TASK_ID in place of the k value. I used 32 processes per job and tried submitting with various amounts of memory requested, from 10-30g. I also added a quality cutoff of 20 (parameter q=20) to this run. The files used this time were concatenated versions of the various sequencing runs for each library: | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R1_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R2_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R1_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R2_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R1_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R2_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz | ||
| + | * /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz | ||
| + | |||
| + | The files had adapters trimmed using SeqPrep, but were not merged (see the data pages for more details). The four libraries used were SW018, SW019, BS-MK, and BS-tag. | ||
| + | |||
| + | I was not able to get these to run successfully. On the first attempt, the job with k=55 started running and died after 6 hours. It was difficult to tell why based on the error (probably ran out of memory) so after this I added the v=-v (verbose) option. Here's the error I got (before verbose option): | ||
| + | |||
| + | <code> | ||
| + | /opt/openmpi/bin/mpirun -np 32 ABYSS-P -k55 -q20 --coverage-hist=coverage.hist -s slug-bubbles.fa - | ||
| + | o slug-1.fa /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R | ||
| + | 1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and | ||
| + | _UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019 | ||
| + | _S1_S2_and_UCSF_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_ | ||
| + | libs/SW019_S1_S2_and_UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPr | ||
| + | ep_newData/UCSF_BS-MK_CATCCGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/S | ||
| + | eqPrep_newData/UCSF_BS-MK_CATCCGG_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimmi | ||
| + | ng/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_t | ||
| + | rimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz | ||
| + | ABySS 1.5.2 | ||
| + | ABYSS-P -k55 -q20 --coverage-hist=coverage.hist -s slug-bubbles.fa -o slug-1.fa /campusdata/BME235/Spr | ||
| + | ing2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R1_trimmed.fastq.gz /campusdata/BME | ||
| + | 235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz | ||
| + | Running on 32 processors | ||
| + | 9: Running on host campusrocks2-0-2.local | ||
| + | 25: Running on host campusrocks2-0-2.local | ||
| + | 2: Running on host campusrocks2-0-2.local | ||
| + | 3: Running on host campusrocks2-0-2.local | ||
| + | 8: Running on host campusrocks2-0-2.local | ||
| + | 10: Running on host campusrocks2-0-2.local | ||
| + | 11: Running on host campusrocks2-0-2.local | ||
| + | 13: Running on host campusrocks2-0-2.local | ||
| + | 27: Running on host campusrocks2-0-2.local | ||
| + | 26: Running on host campusrocks2-0-2.local | ||
| + | 7: Running on host campusrocks2-0-2.local | ||
| + | 12: Running on host campusrocks2-0-2.local | ||
| + | 28: Running on host campusrocks2-0-2.local | ||
| + | 14: Running on host campusrocks2-0-2.local | ||
| + | 18: Running on host campusrocks2-0-2.local | ||
| + | 6: Running on host campusrocks2-0-2.local | ||
| + | 22: Running on host campusrocks2-0-2.local | ||
| + | 30: Running on host campusrocks2-0-2.local | ||
| + | 23: Running on host campusrocks2-0-2.local | ||
| + | 24: Running on host campusrocks2-0-2.local | ||
| + | 1: Running on host campusrocks2-0-2.local | ||
| + | 17: Running on host campusrocks2-0-2.local | ||
| + | 19: Running on host campusrocks2-0-2.local | ||
| + | 0: Running on host campusrocks2-0-2.local | ||
| + | 16: Running on host campusrocks2-0-2.local | ||
| + | 4: Running on host campusrocks2-0-2.local | ||
| + | 15: Running on host campusrocks2-0-2.local | ||
| + | 29: Running on host campusrocks2-0-2.local | ||
| + | 31: Running on host campusrocks2-0-2.local | ||
| + | 5: Running on host campusrocks2-0-2.local | ||
| + | 20: Running on host campusrocks2-0-2.local | ||
| + | 21: Running on host campusrocks2-0-2.local | ||
| + | 0: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R1_trimmed.fastq.gz'... | ||
| + | 2: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R1_trimmed.fastq.gz'... | ||
| + | 3: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R2_trimmed.fastq.gz'... | ||
| + | 7: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz'... | ||
| + | 4: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R1_trimmed.fastq.gz'... | ||
| + | 1: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R2_trimmed.fastq.gz'... | ||
| + | 5: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R2_trimmed.fastq.gz'... | ||
| + | 6: Reading `/campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz'... | ||
| + | -------------------------------------------------------------------------- | ||
| + | mpirun noticed that process rank 0 with PID 8806 on node campusrocks2-0-2.local exited on signal 9 (Killed). | ||
| + | -------------------------------------------------------------------------- | ||
| + | make: *** [slug-1.fa] Error 137 | ||
| + | </code> | ||
| + | |||
| + | The job ran for about 6 hours before being killed, according to qacct. | ||
| + | |||
| + | For all other jobs in the array, and for other tries using the same submission script, the jobs never started running, and I got this error: | ||
| + | |||
| + | <code>/opt/openmpi/bin/mpirun -np 32 ABYSS-P -k57 -q20 --coverage-hist=coverage.hist -s slug-bubbles.fa -o slug-1.fa /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW018_S1_and_UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_catted_libs/SW019_S1_S2_and_UCSF_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-MK_CATCCGG_R2_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R1_trimmed.fastq.gz /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep_newData/UCSF_BS-tag_GTAGAGG_R2_trimmed.fastq.gz | ||
| + | error: executing task of job 81112 failed: execution daemon on host "campusrocks2-0-1.local" didn't accept task | ||
| + | -------------------------------------------------------------------------- | ||
| + | A daemon (pid 43664) died unexpectedly with status 1 while attempting | ||
| + | to launch so we are aborting. | ||
| + | |||
| + | There may be more information reported by the environment (see above). | ||
| + | |||
| + | This may be because the daemon was unable to find all the needed shared | ||
| + | libraries on the remote node. You may set your LD_LIBRARY_PATH to have the | ||
| + | location of the shared libraries on the remote nodes and this will | ||
| + | automatically be forwarded to the remote nodes. | ||
| + | -------------------------------------------------------------------------- | ||
| + | -------------------------------------------------------------------------- | ||
| + | mpirun noticed that the job aborted, but has no info as to the process | ||
| + | that caused that situation. | ||
| + | -------------------------------------------------------------------------- | ||
| + | -------------------------------------------------------------------------- | ||
| + | mpirun was unable to cleanly terminate the daemons on the nodes shown | ||
| + | below. Additional manual cleanup may be required - please refer to | ||
| + | the "orte-clean" tool for assistance. | ||
| + | -------------------------------------------------------------------------- | ||
| + | campusrocks2-0-1.local - daemon did not report back when launched | ||
| + | campusrocks2-0-2.local - daemon did not report back when launched | ||
| + | make: *** [slug-1.fa] Error 1 | ||
| + | </code> | ||
| + | |||
| + | It seems like the ABySS group in a previous iteration of the class had the same issue. I submitted an IT ticket and received absolutely no help. The only thing I could figure out is that this is some sort of issue with openmpi, so our next steps will be attempting the assembly using orte instead of openmpi and also trying the assembly on edser2. We are also going to try some end trimming first so that we have a better chance of not using up all the available memory. | ||
| + | |||
| + | |||
| + | The output and log files for this assembly are in /campusdata/BME235/S15_assemblies/abyss/sidra/assembly and /campusdata/BME235/S15_assemblies/abyss/sidra/assembly/failed_runs. | ||
| + | |||
| + | |||
| + | |||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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