Filtlong and Flye

Question

[awhale01]

Hi,

I am trying to run Flye on some filtered Fastq files of ONT reads. I am using Filtlong for some light QC before running Flye. One issue I am running into is that after running Filtlong, Flye throws an invalid char error on the filtered fastq. After giving Fastqc the filtered fastq to see what was wrong it then throws a Midline '....' didnt start with '+'. The Filtlong outfile also contains text before the reads, but the invalid char error still persists after removing these leading lines. The original unfiltered fastq does not throw any errors with Fastqc so this must be something Filtlong is doing? Does anyone have any ideas for a work around for this or why Filtlong is doing this?

Thank you!

[h.mon]

What is the exact command-line you are using for Filtlong? What kind of "text before the reads" the output contain? Copy / paste the command and a snippet of the "text" appearing in Filtlong output.

[awhale01]

My Filtlong command is, filtlong -p 95 --min_length 1000 inFastq.fastq > Filtered.fastq

The extraneous lines before the reads are: Scoring Reads; Read count: "list of reads"; target: "-t integer"; keeping "read amount kept" ; Outputting Reads.

This is by memory as my instance is currently down.

For context I am trying to run Trycycler. On their GitHub this is the way they use Filtlong as well before using Flye as one of the Trycycler assemblers. I have used Filtlong with Unicycler without issue prior to this.

[h.mon]

It seems standard error is being redirected to the Filtered.fastq file. Are you running Filtlong with nohup, or inside some script?

[awhale01]

I am running it on its own command, without using nohup. When checking the lines specified by the midline error I see that in that location the fastq is not following the convention of;

@1aaa54c7..... 
CTACTATACC.....
+
$%//226415

Instead it looks like this;

@30512bf0...
AAGAATCAC....
CGCGCTGCT... <---- There is an extra sequence here
+
6'*0212/...... < --- and there is an extra line between here and the next @ line identifier
$%%%$%%%#.....