Inconsistant fastq-mcf between servers about ea-utils HOT 8 CLOSED

I have just tried the following: copy the binary from m1 to m2, and run the 
m1's fastq-mcf on m2: it works. Something specific to m2 happens during the 
compilation (gcc does not produce any error message during the compilation of 
fastq-mcf). 

Also, version ea-utils.1.1.2-484 does not have this problem on m2

is it possible for you to post the adapters files and at least a subset of the 
fastq's with the incorrect behavior?  i'm running those same Ubuntu gcc version 
on several boxes.

Have you tried just getting the "latest version"?   r600+ ?

Hi,
I just tested the latest SVN version, and using the same example got:

zgrep -c AAGCAGTGGTATCAACGCAGAGTACTTTTT test1.fastq.gz
817

(expected is 0, and raw data gives: 92403)

So that's much better. I still wonder why ~800 out of the 92403 adapters still 
find their way to the output...

My adapter file is the following:

>MINTadapterFiveprime
AAGCAGTGGTATCAACGCAGAGTACGGGGG
>MINTadapterThreeprimeA
AAGCAGTGGTATCAACGCAGAGTACTTTTT
>PE1adapter
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
>PE2adapter
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE1PCRprimer
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PE2PCRprimer
CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
>Illumina_Multiplexing_PCR_Primer_2.01
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>C_Illumina_Multiplexing_PCR_Primer_2.01
AGATCGGAAGAGCACACGTCTGAACTCCAGTC
>adapThreep_TAGATG
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGATGATCTCGTATGCCGTCTTCTGCTTG
>adapThreep_CTTGTA
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
>adapThreep_GGCTAC
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
>adapThreep_ATCACG
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>Mint2-Threep-CDS-4M adapter
AAGCAGTGGTATCAACGCAGAGTGGCCGAGGCGGCCTTTTGTTTTTTCTTTTTTTTTTTTT
>C_adapFivep
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
>C_MINT2-Fivep-PlugOligo-3M-adapter
CCCCCGGCCGTAATGGCCACTCTGCGTTGATACCACTGCTT
>C_MINT2-Fivep-PlugOligo-1-adapter
CCCGCGTACTCTGCGTTGATACCACTGCTT
>C_MINT1adapterFiveprime
CCCCCGTACTCTGCGTTGATACCACTGCT


Best,

i'm guessing that those adapters are either a) not at the end or b) masked by 
too much mismatch?

... but that's just a guess.  i'd need to see the stderr output as well, and 
would really like to be able to run in a debug mode on the original file, and 
try to isolate the reads that are an issue, etc.

Can't reproduce.  No resp in 2 months, closing.