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Are the alignments produced by Seal Seqal equivalent to this produced by BWA?

Yes...but it depends. Seqal internally uses the alignment code from BWA (version 0.5.10 as of this writing). BWA has since progressed since that version, in particular with the introduction of the BWA-mem algorithm. At the moment Seqal does not include this algorithm and still uses BWA-SW. There are plans to update the internal version in BWA.

To verify the correctness of Seqal’s output, we aligned a data set consisting of 5 million read pairs (the first 5M from run id ERR020229 of the 1000 Genomes Project [1]) to the UCSC HG18 reference genome [2] with both Seal ver. 0.1.0 and BWA ver. 0.5.8c. With BWA, we ran bwa aln and bwa sampe, while with Seal we ran the PairReadsQseq and Seqal applications.

We compared the resulting mappings, and observed that the result was identical for 99.5% of the reads. The remaining 0.5% had slightly different map quality scores (mapq), while the mapping coordinates were identical for all but two reads. The latter two cases both had multiple best hits, but resulted in different alignment choices probably due to insert size statistics, in turn due to the particular input read batch. Slight differences in mapq scores are expected because their calculation takes into account the insert size statistics, which are calculated from windows of the sample of sequences BWA analyses. Since the sample windows seen by the command line version of BWA and Seal are different for each read, a slight change in the mapq value is expected. To verify this hypothesis, we ran BWA with varying input data sets while keeping 3000 of those reads that produced mapq variations in the original experiment. We observed that the mapq values for those reads varied between runs.

Can I output a file in BAM format?

For the moment, you can’t generate BAM files from directly from the Hadoop jobs, but you can create one on-the-fly as you download your output from HDFS.

For instance, you can merge and download all part SAM files with seal merge_alignments:

seal merge_alignments --annotations=file://${RefPath}.ann read_sort_output_dir

The command above will write a proper SAM to standard output. Therefore, you can pipe it to samtools, and have it generate a BAM on-the-fly:

seal merge_alignments --annotations=file://${RefPath}.ann read_sort_output_dir | \
  samtools view -bST  ${RefPath}.fai /dev/stdin -o final_output.bam

Unfortunately this method is relatively slow, because the BAM is created serially on one machine. An ideal solution would be to have ReadSort optionally output parts of the BAM file, whose computation would be distributed and thus fast, and then merge those parts at the end as necessary. Alas we haven’t implemented this solution yet.

How do I decide how many reduce tasks to use?

You should follow the standard Hadoop advice to set the number of reduce tasks in which to split your problem. Generally, it should be a multiple of the number of reduce tasks your cluster can run simultaneously, minus a few to allow for tasks that may fail and have to be ru-run by Hadoop. By choosing the number of reduce tasks in this manner you can avoid situations where the end of your job is held up by a few stragglers. For instance, if your cluster is configured with 5 reduce slots per node, and has 10 nodes, try using 48 reduce tasks.

If the input is too big, you may find that the reducers require too much memory to complete the job in one reduce iteration. In this case, double the number of reduce tasks to 96.

If you don’t specify the number of reduce tasks to use, Seal programs will choose a number based on the number of active nodes in the cluster (usually 3 or 6, depending on the type of workload the program creates).

I launched Seqal a few minutes ago but the JobTracker still doesn’t show it as “running”

Before Hadoop starts running the seqal job it needs to copy the reference to all worker nodes. It’ll take a few minutes (as many as 15 depending on the reference you’re using and the speed of your cluster).

In the meantime, you should be able to see the job in queue. From the main JobTracker page, under “Scheduling Information” -> “Queue name” click on your queue (probably “default”). You should see the seqal job in the waiting list.

[1]Durbin, R. M., Altshuler, D. L., et al. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061–1073.
[2]Fujita, P. A., Rhead, B., et al. (2010). The UCSC Genome Browser database: update 2011. Nucleic Acids Res.