Error: fxtools qa

[aerusakovich]

Hello, YanGao!

I was trying to run isocirc on my data, but got an error in fxtools step:

Running isocirc on data
== 10:47:21-May-07-2024 == [check_dependencies] Checking dependencies ...
== 10:47:21-May-07-2024 == [check_dependencies] All dependencies satisfied!
== 10:47:21-May-07-2024 == [Tandem-Repeats-Finder] Finding tandem repeats with TRF ...
== 10:47:21-May-07-2024 == [fxtools] fxtools qa /groups/dog/anastasia/data/data_ciri-long/CRR194209.fq > /groups/dog/anastasia/results/isocirc/data_ciri-long/long_reads.fa 2> /dev/null
== 10:47:21-May-07-2024 == [fxtools] Error: fxtools qa /groups/dog/anastasia/data/data_ciri-long/CRR194209.fq > /groups/dog/anastasia/results/isocirc/data_ciri-long/long_reads.fa 2> /dev/null
Done

What could be done to fix it?

Here is how I run it:

# Activate env
conda activate isocirc

#Paths
data_name="data_ciri-long"
output_dir="/groups/dog/anastasia/results/isocirc/$data_name"
reads_path="/groups/dog/anastasia/data/data_ciri-long/CRR194209.fq"
ref_path="/groups/dog/anastasia/nanosim/GRCm39.genome.fa.gz"
gene_anno_path="/groups/dog/anastasia/nanosim/gencode.vM34.annotation.gtf.gz"
gtf_path="/groups/dog/anastasia/nanosim/gencode.vM34.annotation.gtf.gz"
#Parameters
THREADS=8
#Run
python /groups/dog/anastasia/progs/isoCirc/isoCirc/isoCirc_pipeline/isocirc/isocirc "$reads_path" "$ref_path" "$gene_anno_path" "$gtf_path" "$output_dir" -t $THREADS

Thank you in advance!

[yangao07]

Looks like the fxtools from isocirc didn't work properly. Can you show me the output of which fxtools and ls -l in your output folder?

[yangao07]

Also, how did you install isocirc? pip install isocric?

[yangao07]

If you didn't pip install and run directly with the python file, the dependenices will not be installed and that causes errors.

[aerusakovich]

I actually had problems with installation: https://github.com/Xinglab/isoCirc/issues/12

And yet, it seems fxtools didn't install.

which: no fxtools in (/home/genouest/cnrs_umr6290/aerusakovich/.conda/envs/isocirc/bin:/local/miniconda3/bin:/local/miniconda3/condabin:/home/genouest/cnrs_umr6290/aerusakovich/.vscode-server/bin/660393deaaa6d1996740ff4880f1bad43768c814/bin/remote-cli:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin)
total 0
-rw-r--r-- 1 aerusakovich cnrs_umr6290 0 May  7 17:30 long_reads.fa

[yangao07]

OK, for your case, you can add the binary path to your $PATH: export PATH="/path/to/isocirc/isoCirc_pipeline/bin:$PATH" or simply copy the files to your local bin dir: cp /path/to/isocirc/isoCirc_pipeline/bin/* ~/.local/bin

[aerusakovich]

Actually had to copy to conda env bin and not local (didn't work with local), but seems to work and pass this step!

cp /groups/dog/anast
asia/progs/isoCirc/isoCirc/isoCirc_pipeline/bin/* ~/.conda/envs/isocirc/bin

TY, YanGao, you are always helpful :)