Sequence dictionaries differ

I’m running:

java -Xmx4g -jar picard.jar CollectRnaSeqMetrics \
REFERENCE_SEQUENCE=hg19.genome.fa \
REF_FLAT=gencode.v19.annotation.refFlat \
RIBOSOMAL_INTERVALS=gencode.v19.rRNA.interval_list \
STRAND_SPECIFICITY=NONE \
INPUT=file.bam \
ASSUME_SORTED=true \
OUTPUT=file.rnaseq_metrics \
CHART_OUTPUT=file.rnaseq.pdf

I get this error:

Exception in thread "main" picard.PicardException: Sequence dictionaries differ in file.bam and gencode.v19.rRNA.interval_list

However, I copied the sequence dictionary from the BAM file. So, the sequence dictionaries are identical.

Here’s the sequence dictionary along with the first 5 lines of the ribosomal intervals file:

@HD     VN:1.4  SO:coordinate
@SQ     SN:chrM LN:16571
@SQ     SN:chr1 LN:249250621
@SQ     SN:chr2 LN:243199373
@SQ     SN:chr3 LN:198022430
@SQ     SN:chr4 LN:191154276
@SQ     SN:chr5 LN:180915260
@SQ     SN:chr6 LN:171115067
@SQ     SN:chr7 LN:159138663
@SQ     SN:chr8 LN:146364022
@SQ     SN:chr9 LN:141213431
@SQ     SN:chr10        LN:135534747
@SQ     SN:chr11        LN:135006516
@SQ     SN:chr12        LN:133851895
@SQ     SN:chr13        LN:115169878
@SQ     SN:chr14        LN:107349540
@SQ     SN:chr15        LN:102531392
@SQ     SN:chr16        LN:90354753
@SQ     SN:chr17        LN:81195210
@SQ     SN:chr18        LN:78077248
@SQ     SN:chr19        LN:59128983
@SQ     SN:chr20        LN:63025520
@SQ     SN:chr21        LN:48129895
@SQ     SN:chr22        LN:51304566
@SQ     SN:chrX LN:155270560
@SQ     SN:chrY LN:59373566
chr1    9497728 9497837 -   ENST00000517147.1
chr1    13949679    13949779    -   ENST00000411020.1
chr1    34578550    34578664    +   ENST00000364278.1
chr1    37730278    37730387    -   ENST00000516559.1
chr1    39619836    39619968    -   ENST00000410446.1

[slowkow]

The problem: my sequence dictionary lines are space-delimited, and they must be tab-delimited, i.e. \t.

I apologize for the confusion, and for wasting your time. I recommend that you document the format of the interval list file, or refer the user to an example of a properly-formatted file. It would be useful to point them to a ready-to-use file like this one.

Strangely, the current documentation for CollectRnaSeqMetrics refers the user to the IntervalList javadoc. The comment at the top of the page does not mention that the SAM-style header must be tab-delimited. In my opinion, developers – not users – should be referred to javadoc documentation.

Wrong (each item is separated by a space ' '):

@SQ SN:chrM LN:16571

Right (each item is separated by a tab '\t'):

@SQ SN:chrM LN:16571

[slowkow]

https://github.com/broadinstitute/picard/issues/126#issuecomment-66618588