[maker-devel] part long scafflods finished，the others failed

[刘昱]

Hello,

        I apologize for not posting directly to the archived forum but it appears that the option to enter new posts is disabled.

        Thank you for your continued support of Maker and your responses to the forum posts. I have been running Maker (V3.01.02) to annotate a apple genome that consists of 17 chromosome-length scaffolds and some small contigs.

        In my various tests in running Maker, the vast majority of the smaller contigs were annotated failed. I'm not sure the long scaffolds finished rather than smaller contigs.

        ```

        open3: fork failed: Cannot allocate memory at /data/liuyu/Software/maker/bin/../lib/File/NFSLock.pm line 1037 thread 1.

        --> rank=3, hostname=localhost.localdomain

       ERROR: Failed while collecting blastn reports

       ERROR: Chunk failed at level:1, tier_type:3

       FAILED CONTIG:scaffold1A

       deleted:0 hits

       ERROR: Chunk failed at level:4, tier_type:0

       FAILED CONTIG:scaffold1A

       ````

       The work in run.log.child.0 is FINISHED. While in the theVoid.scaffold1A/run.log.child.1, the error code showed below:

       ```

       STARTED CF_hap1_part3_rnd1.maker.output/CF_hap1_part3_rnd1_datastore/67/D7/scaffold1A//theVoid.scaffold1A/0/scaffold1A.1.66268.0.db%2E1-66268%2Efor_blastn%2Efasta.blastn

       DIED    RANK    3:4:0:2

       DIED    COUNT   1

       ````

      My command is "mpiexec -n 8 /data/liuyu/Software/maker/bin/maker -base CF_hap1_part3_test part3_round1_maker_opts.ctl maker_bopts.ctl maker_exe.ctl". The mpiexec is used by MPICH(v3.3.2). And When I test and use the MPICH2, the error is same. Meanwhile, when I use less number of processes, the task is failed too.

      Thanks for any troubleshooting tips you can offer.

Best wishes,

Yu Liu

 

[Carson Holt]

You are out of RAM. If running on a scheduler like SLURM or PBS, depending on how you submit the job and how the scheduler has been configured, you may not have access to the whole machine’s RAM (you may need to request an amount of RAM).  Also make sure /tmp or the location you specify as TMP= is not an in memory directory (not uncommon on some configurations).  On the cluster where I work for example /tmp defaults to in memory, and real disk temporary space is at /scratch/local, so I must specify that detail in the maker_opts.ctl file in the TMP= value.

Other things to look at —>

1. If running under MPI, cpu= in maker_opts.ctl must be set to 1.
2. max_dna_len= should be 100000 (the default)
3. In maker_bopts.ctl, set all the depth_blast= options to something like 10 or 20 (there are 3 depth values you will have to set). The default is to keep everything, and if you have really deep alignments that can use a lot of RAM with out any actual benefit for gene prediction.

—Carson

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