Installed BUSCO is detected to be missing

yifangt commented 3 years ago

Hello, I met a problem with GUESSmyLT:

$ Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   bowtie2_index
    1   bowtie2_map
    1   check_programs
    1   inferr
    1   samtools_sort_new_mapped
    1   subsample_fastq
    6

[Thu Oct  7 14:33:03 2021]
rule check_programs:
    output: programs.checked
    jobid: 3
    priority: 2

Job counts:
    count   jobs
    1   check_programs
    1
[Thu Oct  7 14:33:03 2021]
Error in rule check_programs:
    jobid: 0
    output: programs.checked

SystemExit in line 25 of /storage/ppl/software/anaconda3/envs/AltSplice/lib/python3.8/site-packages/guessmylt-0.2.5-py3.8.egg/GUESSmyLT/check_programs:
1
  File "/storage/ppl/software/anaconda3/envs/AltSplice/lib/python3.8/concurrent/futures/thread.py", line 57, in run
  File "/storage/ppl/software/anaconda3/envs/AltSplice/lib/python3.8/site-packages/guessmylt-0.2.5-py3.8.egg/GUESSmyLT/check_programs", line 25, in __rule_check_programs
  File "/storage/ppl/software/anaconda3/envs/AltSplice/lib/python3.8/_sitebuiltins.py", line 26, in __call__
Exiting because a job execution failed. Look above for error message
Checking for bowtie2, upon error make sure it's installed properly
Bowtie2 works, continuing...

Checking for BUSCO, upon error make sure it's installed properly
Let's try run_busco
Let's try run_BUSCO.py
BUSCO is missing.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /storage/yifang/AltSplicing/scripts/.snakemake/log/2021-10-07T143303.312906.snakemake.log

The log pointed to me the problem busco, but busco was installed.

$ which busco
/storage/ppl/software/anaconda3/envs/AltSplice/bin/busco

My command line is:

GUESSmyLT  --reads ${DIR_IN}/RE5_1_trimmed_PE_R1.fq.gz ${DIR_IN}/RE5_1_trimmed_PE_R2.fq.gz \
             --reference ${REF_FASTA} \
             --mapped ${DIR_OUT}/Brapa_genome_1st_sorted.bam \
             --mode genome \
             --annotation ${GFF} \
             --organism euk

I am wondering is anybody has a clue for this issue? Thanks a lot!

Juke34 commented 3 years ago

What version of BUSCO do you use. Try busco 3.0.2, it is working with that one for sure

yifangt commented 3 years ago

Thank Jacques! My BUSCO was 5.2.2 However, installation with 3.0.2 did not create executable busco/BUSCO, which is no where to be found.

$ conda install -c conda-forge -c bioconda busco=3.0.2 
$ which busco 
$

Tried to manully install busco=3.0.2, but could not locate the source code of busco 3.0.2 from https://busco.ezlab.org/ Any clue again? Thanks!

Juke34 commented 3 years ago

To call it (at least with that version) on conda, it is something like "run_busco.pl" and not "busco" Did you try the pipeline? it should work

NBISweden / GUESSmyLT

Installed BUSCO is detected to be missing #19