trouble parsing problem filterbytile

Question

[charles.decraene.unistra]

Hello I have a problem with filterbytile : I try to analyze the data from GSE52778 I use filterbytile.sh and It seems I have a "Trouble parsing problem"

when I try : f

ilterbytile.sh in1=SRR1039508_1.fastq in2=SRR1039508_2.fastq out1=SRR1039508_1_filtre.fastq out2=SRR1039508_2_filtre.fastq

I obtain :

java -ea -Xmx6678m -Xms6678m -cp /XXXX/XXXX/bin/bbmap/current/ hiseq.AnalyzeFlowCell in1=SRR1039508_1.fastq in2=SRR1039508_2.fastq out1=SRR1039508_1_filtre.fastq out2=SRR1039508_2_filtre.fastq
Executing hiseq.AnalyzeFlowCell [in1=SRR1039508_1.fastq, in2=SRR1039508_2.fastq, out1=SRR1039508_1_filtre.fastq, out2=SRR1039508_2_filtre.fastq]

Set INTERLEAVED to false
Loading kmers:      205.432 seconds.
Filling tiles:      Trouble parsing header SRR1039508.1.1 HWI-ST177:290:C0TECACXX:1:1101:1225:2130 length=63
java.lang.AssertionError: SRR1039508.1.1 HWI-ST177:290:C0TECACXX:1:1101:1225:2130 length=63
    at hiseq.IlluminaHeaderParser.parseInt(IlluminaHeaderParser.java:149)
    at hiseq.IlluminaHeaderParser.parseCoordinates(IlluminaHeaderParser.java:71)
    at hiseq.IlluminaHeaderParser.parse(IlluminaHeaderParser.java:55)
    at hiseq.FlowCell.getMicroTile(FlowCell.java:144)
    at hiseq.AnalyzeFlowCell.fillTilesInner(AnalyzeFlowCell.java:641)
    at hiseq.AnalyzeFlowCell.fillTiles(AnalyzeFlowCell.java:380)
    at hiseq.AnalyzeFlowCell.process(AnalyzeFlowCell.java:316)
    at hiseq.AnalyzeFlowCell.main(AnalyzeFlowCell.java:51)

thanks for your help

C

[Pierre Lindenbaum]

see C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias

[charles.decraene.unistra]

I did it (fatq-dump -F XXXXXXXXX) I i obtain the same thing.......

Loading kmers: 7.484 seconds.

**Filling tiles:    Trouble parsing header HWI-ST177:290:C0TECACXX:1:1101:1225:2130**

java.lang.StringIndexOutOfBoundsException: String index out of range: 40
    at java.base/java.lang.StringLatin1.charAt(StringLatin1.java:47)
    at java.base/java.lang.String.charAt(String.java:693)
    at hiseq.IlluminaHeaderParser.goBackSeveralColons(IlluminaHeaderParser.java:133)
    at hiseq.IlluminaHeaderParser.parseCoordinates(IlluminaHeaderParser.java:70)
    at hiseq.IlluminaHeaderParser.parse(IlluminaHeaderParser.java:55)
    at hiseq.FlowCell.getMicroTile(FlowCell.java:144)
    at hiseq.AnalyzeFlowCell.fillTilesInner(AnalyzeFlowCell.java:641)
    at hiseq.AnalyzeFlowCell.fillTiles(AnalyzeFlowCell.java:380)
    at hiseq.AnalyzeFlowCell.process(AnalyzeFlowCell.java:316)
    at hiseq.AnalyzeFlowCell.main(AnalyzeFlowCell.java:51)

Answer 1

[GenoMax]

It appears that this data has been submitted to SRA stripping the index information from the header. So to get around that you should first use reformat.sh to add 1: and 2: to the fastq headers.

You can do that by

 reformat.sh addcolon=t in1=SRR1039508_1.fastq in2=SRR1039508_2.fastq out1=test1.fastq out2=test2.fastq

That will give you

@HWI-ST177:290:C0TECACXX:1:1101:2225:2087 1:
AACAAGAAGAGTTCTCTGAAAGGCAATGAGAAAGAGAAGGAGAAACAACAGCGGGAGAAGGAT
+
HJJJJJJJJJJFIIIJJJJJJJJIJJJJHJJJJJJJJJJJJJJJIJJJJIJJHHFDDDDDDDD

You can then run filterbytile.sh with these intermediate files.

filterbytile.sh in1=test1.fastq in2=test2.fastq out1=final_R1.fastq.gz out2=final_R2.fastq.gz