picard-tools 1.140 interval file error

[cmccabe]

When I create a standard 6 column bed, picard throws the error:

 Exception in thread "main" htsjdk.samtools.SAMException: Invalid interval record contains 6 fields: chr1    955543    955763    AGRN-6|gc=75    0    +

When I use the same format that was used in 1.139 picard throws this error:

Exception in thread "main" java.lang.IllegalArgumentException: Invalid strand field: 
	at htsjdk.samtools.util.IntervalList.fromReader(IntervalList.java:467)
	at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:381)
	at htsjdk.samtools.util.IntervalList.fromFiles(IntervalList.java:410)
	at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:85)

TI=
@HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
chr1	955543	955763	+	AGRN-6|gc=75
chr1	957571	957852	+	AGRN-7|gc=61.2

BI=
@HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
chr1	955542	955662	+	AGRN_70
chr1	955643	955763	+	AGRN_71

Did something change in the way the command is used?

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar /home/cmccabe/Desktop/NGS/picard-tools-1.140/picard.jar CalculateHsMetrics BI=/home/cmccabe/Desktop/NGS/bed/picard/unix_sam_sorted_xgen_baits.bed TI=/home/cmccabe/Desktop/NGS/bed/picard/unix_sam_sorted_xgen_targets.bed I=IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader.bam O=/home/cmccabe/Desktop/NGS/IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader_all_IDT.CalculateHSmetrics

[GenoMax]

Also posted at: https://www.biostars.org/p/165002/

I thought we had got this working in a previous thread, if I recollect right.

[cmccabe]

It was working in 1.139 and then I upgraded to 1.140. Using the same format that worked in 1.139 throws that error. Thank you .

[GenoMax]

It is strange that a minor version upgrade would cause this problem. Have you looked at the release notes for 1.140 to see if something is mentioned specifically about this change? You can always run the older version and get the result you need.

[cmccabe]

The same error appear in 1.139, so it appears that the TI and BI files are not formatted correctly.

I will look into them more, there were sent to me so maybe there was an error in the transfer. Thank you .

[GenoMax]

Look for white spaces etc. in odd places (like @kmcarr had found last time).

[cmccabe]

There was no issue with picard. The files were originally created in excel with the 4th column being right justified/indented. So when the windows line endings were removed there was a trailing space, that was causing the issue. Once removed there was no problem. Thank you .

[kmcarr]

There was no issue with picard. The files were originally created in excel with the 4th column being right justified/indented. So when the windows line endings were removed there was a trailing space, that was causing the issue. Once removed there was no problem. Thank you .

Reason # 5,481,536 to never, ever use Excel for bioinformatics.

[cmccabe]

That is very true . Thank you.