Fastxtoolkit nucleotide distribution issue

[jeny]

Hi all,
I need some help on fastx-toolkit use.
I would like to generate nucleotide distribution line graph but I don't manage.
Below is command lines that I used :
1-to obtain statistics report
cat ../../sequences/phix/s_4_1_sequence.txt | fastx_quality_stats -o ../../sequences/phix/s_4_1_qual_stat.txt

2-to create distribution graph
fastx_nucleotide_distribution_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_s_4_1.png

that worked.

3-to create distribution line graph
fastx_nucleotide_distribution_line_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_line_s_4_1.png

It returned:
Error: Input file is not a valid statistics report.
This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.
In Galaxy,
Please use the "Compute Quality Statistics" tool (in the "NGS: QC and Manipulation" category) to compute the quality statistics report, and then use this tool with the new statistics report.
On the command line,
Please use the "fastx_quality_stats" program to create the statistics report.

I thought both distribution scripts work similary and have only different output graphs. Maybe I am wrong.
Why does it work in one case and not in the other with same statistics report file as input ?

Thanks for help.
Jennifer

[tdoniger]

Fastxtoolkit nucleotide distribution issue

Hi,

I don't know if it is correct, but I just commented out the lines of the file check from the shell file and it works without any problem.

Good luck!
Tirza

[jeny]

Hi Tirza,

I commented lines that you suggested and it works.

Many thanks,
Jennifer

[rain bow]

encountering the same problem

Please help me too...as I am encountering the same problem while using fastq quality box plot.sh
This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.

[alexsf]

Hi,

You don't have to comment it. In line 121 make this change:

AWK_VALID_STAT='NR==1 && $1=="column" && $2=="count" && $3=="min" { exit 2 } NR>1 { exit}'

The problem is that they put "cycle" instead of "column" which is the right header for the qual stats file.

Cheers.