optimuscoprime / autoadapt Goto Github PK

I get the following error while doing a make install:

At least Python 2.6 is required.
make: *** [install] Error 1

Even though the default python version installed is 2.7.6:

swe@grid01: /home/volatile/swe/soft/autoadapt-master$ python
Python 2.7.6 (default, Jan 31 2014, 14:21:21)

Using Perl 5.24.1.

Doing just "autoadapt.pl" with no arguments to print help message. Get this error and autoadapt.pl exits:

Experimental keys on scalar is now forbidden at ./autoadapt.pl line 523.

After fixing it by adding "%" at the proper position, get:

Experimental keys on scalar is now forbidden at ./autoadapt.pl line 534.

I don't really know Perl, and I think the "%" is the fix from reading this: http://stackoverflow.com/a/29614053

Hi,
when adaptor trimming on paired end data, its possible that 1 read will become too short and get discarded. If i'm not mistaken, its important that the remaining read from the pair in the other file get discarded too (or stored in another file) so that the paired read files stay in sync (same # reads in the same order). This is something that trimgalore attempts to do (though in my hands trim galore keeps on creating corrupt fq.gz files)...

the error i am getting is here:
./autoadapt.pl --minimum-length=16 MiR1_NoIndex_L006_R1_001.fasta mir184_trim.fa

/home/ubuntu/softwares/autoadapt-master/tools/fastqc --threads 1 --outdir /home/ubuntu/softwares/autoadapt-master/autoadapt.tmp.4CkfuyRX /home/ubuntu/mir_gast_analysis/MiR1_NoIndex_L006_R1_001.fasta
Can't open FastQC report at /home/ubuntu/softwares/autoadapt-master/./autoadapt.pl line 378.
I am not sure why it is not taking path correctly.

Hi optimuscoprime,
fastqc 0.10.1 doesn't have the Illumina Nextera adaptor sequences in the contaminants file. But, it does have a --contaminants flag, which allows you to specify a custom contaminants txt file. It would be great if autoadapt accepted that param, and passed it on to fastqc.

perl autoadapt.pl first.fastq.gz clean.fastq.gz
Can't open FastQC report at autoadapt line 378

hello,

When splitting of the fastq files is made, fastq files which do not follow the standard of starting with '@' are created and cutadapt raises an error. Is it possible to modify this? Thank you

Eva