sheinasim / hifiadapterfilt Goto Github PK

Hi!

I am trying to run this tool on my PacBio reads but I get a general error from blast (like if some options are not compatible) that makes me think that maybe there is a problem with my blast version.
What is the recommended version for blast to use?

Thanks!!

fastq.gz and fasta.gz are default outputs for IIe system, make option to work directly from them

would it be possible to add a --cite or --version to the script? it'd make integration into our pipelines that much easier.

Hey, @sheinasim I can't relate to the error the tool throws at me.

This is my command:
sh hifiadapterfilt.sh -p /data01/mlandi/TME117-assembly/filtered.data/filtered.cell1.fastq.gz -t 32 -o filtered.adapter

Kindly assist, Do I miss parameters?

Thanks for this nice tool. Just a quick question. Does HiFiAdapterFilt perform better if I run it on one large input file? Or would it be better to split my input file in several smaller fastq.gz files (for example with fastqsplitter), which I then store in one directory on which I let HiFiAdapterFilt run?

Dear @sheinasim
Thanks for your solution of adapters.
Is there anyway to accept fasta file type for HiFi reads ?

Looking forward to reply.

Best
Johnson

Hi,
I am trying to run HiFiAdapterFilt on a raw PacBio hifi .bam file using the following command:

bash pbadapterfilt.sh -p /path/to/bam/220209_hifi_reads.bam -o HiFiAdaptFilt_220209

and I keep getting the following error:
path/to/bam/220209_hifi_reads.bam.temp_file_list: No such file or directory

It seems to be making the output directory, but cuts out immediately. Do you know what could be going on here?

What are the typical run times for the pipeline? I have a 40GB fastq and I expect it could be anywhere from 5-15 hours, based on transfer rates.

I encountered an error:

BLAST Database error: No alias or index file found for nucleotide database [/pacbio_vectors_db] in search path [/home/liangc/Downloads/PacBio:/scratch/ncbi_blast+/db:]

To solve this problem, I have tried two approaches
(1): Inside my /Downloads/PacBio folder, I created a folder named "pacbio_vectors_db" and put all relevant files within this folder
(2): Inside my /Downloads/PacBio folder, places all individual files that I copied from HiFiAdapterFilt-master/DB/.

Both approaches do not work.

In my .bashrc file, I have put these commands:

export BLASTDB=/scratch/ncbi_blast+/db/
export PATH=$PATH:/home/liangc/Software/HiFiAdapterFilt-master
export PATH=$PATH:/home/liangc/Software/HiFiAdapterFilt-master/DB
export PATH=$PATH:/home/liangc/Downloads/PacBio/pacbio_vectors_db

delete big fasta and fastq files (unzipped or bam converted files)

Hi Sheina,

I was eager to try your adapter trimming tool but I experienced some issues I thought you might want to know about.

I noticed in the 2.0.0 release that line 6 is:
DBpath=$(echo $PATH | sed 's/:/\n/g' | grep "HiFiAdapterFilt/DB" | head -n 1)

However, I think it should be:
DBpath=$(echo $PATH | sed 's/:/\n/g' | grep "HiFiAdapterFilt-2.0.0/DB" | head -n 1)

That still isn't solving a problem I'm having, though. I'm consistently getting the following error unless I hard-code the path to the blast database:

BLAST Database error: No alias or index file found for nucleotide database [/pacbio_vectors_db] in search path [/grps2/kmk/2022-04-20_Ap212/PB744_AP212_5C_ULTP/r64069_20220330_183728/C1/outputs/adapter_filter_test::]

Also, do you know if the adapters used in the ultra-low PacBio library prep are the same as the ones in the pacbio_vectors_db file?

Thanks!
Kevin

count of filtered files ends up in stderr, could write into stats.txt output instead?

Does HiFiAdapterFilt apply to the HiFi data derived from Revio platform?