generate_ska_alignment.py problem

[aslangabriel]

Hi，I prepared fastq-list files as follows JSAHVC01R1 /home/work/APECSRA/JSAHVC01R1.fastq JSAHVC01R2 /home/work/APECSRA/JSAHVC01R2.fastq JSAHVC02R1 /home/work/APECSRA/JSAHVC02R1.fastq JSAHVC02R2 /home/work/APECSRA/JSAHVC02R2.fastq JSAHVC03R1 /home/work/APECSRA/JSAHVC03R1.fastq JSAHVC03R2 /home/work/APECSRA/JSAHVC03R2.fastq JSAHVC04R1 /home/work/APECSRA/JSAHVC04R1.fastq JSAHVC04R2 /home/work/APECSRA/JSAHVC04R2.fastq JSAHVC05R1 /home/work/APECSRA/JSAHVC05R1.fastq JSAHVC05R2 /home/work/APECSRA/JSAHVC05R2.fastq JSAHVC06R1 /home/work/APECSRA/JSAHVC06R1.fastq JSAHVC06R2 /home/work/APECSRA/JSAHVC06R2.fastq, with python editon of 3.6.X. The command line is "python generate_ska_alignment_.py --reference ./CP004009_1.fasta --fastq fastqlist.txt --out APEC.aln"

But it prompted the errot that"Traceback (most recent call last): File "generate_ska_alignment_.py", line 126, in if os.path.isfile(info[1]) and os.path.isfile(info[2]): IndexError: list index out of range ". I have no idea what't the problem. Would you mind fixing it ?

[nickjcroucher]

The forward and reverse FASTQs need to be on the same line. e.g.: JSAHVC01R1 /home/work/APECSRA/JSAHVC01R1.fastq /home/work/APECSRA/JSAHVC01R2.fastq

I should allow for single FASTQ files generally though.

[aslangabriel]

Thanks for your help. By the way for fastq list, am I right to set three columns separated by tab with ID R1path R2 path?