Engine problems

Troubleshooting principles

If the MARTi Engine doesn’t seem to be working, there are a number of places to go to work out what is going wrong:

The output to screen, or if using SLURM, the out/err log files.
The MARTiEngine log - found as sampledir/logs/engine.txt.
The MARTiEngine scheduler log - found as sampledir/logs/scheduler.txt.

BLAST problems

BLAST problems can often be diagnosed by looking at the screen output. For example:

Warning: Error message found in /mnt/shared/projects/LocationSampling/LonCol_Pool2_12092019/marti/logs/megablast_nt/barcode06/fastq_runid_1fec5f69d7b44c09bd896163c8d8b9fd176f2adb_0_filtered_812.log
Message is BLAST Database error: No alias or index file found for nucleotide database [/mnt/shared/projects/LocationSampling/240615_rerun/3_marti/blast_nt_ln/nt] in search path [/mnt/shared/projects/LocationSampling/240615_rerun/3_marti::]
Please check results carefully.

Messages like these come straight from BLAST and problems can be diagnosed without reference to MARTi. In the example above, there are missing BLAST files in the specified database path.

Java heap problems

For large samples, it’s possible that the Java heap size will be exceeded. This might result in exceptions similar to the example below:

Exception in thread "pool-1-thread-1" java.lang.OutOfMemoryError: Java heap space
        at java.base/java.util.Arrays.copyOf(Arrays.java:3481)
        at java.base/java.util.ArrayList.grow(ArrayList.java:238)
        at java.base/java.util.ArrayList.grow(ArrayList.java:245)
        at java.base/java.util.ArrayList.add(ArrayList.java:484)
        at java.base/java.util.ArrayList.add(ArrayList.java:497)
        at uk.ac.earlham.marti.filter.ReadFilterSample.processFile(ReadFilterSample.java:340)
        ...

In this case, you may need to edit the Java heap parameters which are specified in the marti file found in the bin directory of the MARTi code. Use a text editor to edit the line that looks something like this:

JAVA_ARGS="-Xms1g -Xmx16g"

The xms parameter specifies the minimum heap size (in this case 1Gb) and the xmx parameter specifies the maximum heap size (16Gb here).