Can't find index size?

[chofman]

I'm running this FastDemultiplexer/FastDemultiplexer.py SampleSheet2.csv 4 Demux/Sample_lane4/ Demultiplexed > stat.txt

and getting this error in the stats.txt

Error: the SampleSheet does not contain entries for the lane provided. IndexSize= 0

As well as this error printed to the screen:

raceback (most recent call last): File "FastDemultiplexer/FastDemultiplexer.py", line 501, in main() File "FastDemultiplexer/FastDemultiplexer.py", line 492, in main demultiplexer=Demultiplexer(sheet,inputDir,outputDir,lane) File "FastDemultiplexer/FastDemultiplexer.py", line 415, in init sheet=SampleSheet(sampleSheet,lane) File "FastDemultiplexer/FastDemultiplexer.py", line 99, in init self.makeIndex() File "FastDemultiplexer/FastDemultiplexer.py", line 151, in makeIndex print("Index1Length= "+str(self.m_index1Length)) AttributeError: SampleSheet instance has no attribute 'm_index1Length'

I'm trying to demultiplex a lane of HiSeq with 4 reads (2 indexes) and each index is 8 bp

My Sample sheet file looks like this:

C1GMPACXX,4,M-C28,none,CGTTGAGT-AGCGTGTA,gDNA,N,100_PE_8_8,Adam,Missy

Any ideas on what is going on?

Thanks!

[sebhtml]

I tested (see 62079e5550dc0185c3655936c31567a0a06c334c ) with the sample sheet line you provided it works.

$ ./issue-4.sh IndexSize= 1089 Index1Length= 8 Index2Length= 8

The index should contain 1089 elements for that single entry:

No mismatch: 1 1 mismatch on the left, 0 on the right: 8_4 = 32 0 mismatch on the left, 1 on the right: 8_4 = 32 1 mismatch on the left, 1 on the right: 8_4_8*4 = 1024 1024+32+32+1 = 1089

The software should match the 4 provided in the command line with the 4 listed in the second column of your file.

$ cat issue-4.sh #!/bin/bash

rm -rf Output

../FastDemultiplexer.py sheet-4.csv 4 Sample_lane1-test Output $ cat sheet-4.csv C1GMPACXX,4,M-C28,none,CGTTGAGT-AGCGTGTA,gDNA,N,100_PE_8_8,Adam,Missy

[chofman]

Hi Sebastian,

Thanks for testing this, I'm wondering if it is a problem with how my read files are labeled then. Currently, I have 60 files each for R1,R2,R3, and R4 labeled like the one below. Is that the structure you use?

HMMIT01_NoIndex_L004_R2_031.fastq.gz

Thank you for your help!

Courtney

On Thu, Apr 25, 2013 at 10:02 AM, Sébastien Boisvert < [email protected]> wrote:

I tested (see 62079e5https://github.com/sebhtml/FastDemultiplexer/commit/62079e5550dc0185c3655936c31567a0a06c334c) with the sample sheet line you provided it works.

$ ./issue-4.sh IndexSize= 1089 Index1Length= 8 Index2Length= 8

The index should contain 1089 elements for that single entry:

No mismatch: 1 1 mismatch on the left, 0 on the right: 8_4 = 32 0 mismatch on the left, 1 on the right: 8_4 = 32 1 mismatch on the left, 1 on the right: 8_4_8*4 = 1024 1024+32+32+1 = 1089

The software should match the 4 provided in the command line with the 4 listed in the second column of your file.

$ cat issue-4.sh #!/bin/bash

rm -rf Output

../FastDemultiplexer.py sheet-4.csv 4 Sample_lane1-test Output $ cat sheet-4.csv C1GMPACXX,4,M-C28,none,CGTTGAGT-AGCGTGTA,gDNA,N,100_PE_8_8,Adam,Missy

— Reply to this email directly or view it on GitHubhttps://github.com/sebhtml/FastDemultiplexer/issues/4#issuecomment-17008721 .

[sebhtml]

In my test, files are like that:

$ find Sample_lane1-test/|grep .fastq.gz Sample_lane1-test/lane1_NoIndex_L001_R1_001.fastq.gz Sample_lane1-test/lane1_NoIndex_L001_R2_001.fastq.gz Sample_lane1-test/lane1_NoIndex_L001_R3_001.fastq.gz Sample_lane1-test/lane1_NoIndex_L001_R4_001.fastq.gz

I use the command

../FastDemultiplexer.py SampleSheet-NOVA.csv 1 Sample_lane1-test Output