Error after fresh conda installation, and error during example run

[desmodus1984]

HI,
I am interested in checking a bat assembly using craq. I installed it using conda. Installation went fine, supposedly, but then it failed when I tried to run it using short-read data that I mapped, and created a bam file with.
I used this code:

craq -g myse-hapog.fasta -ngs MYSE.Q20.mapped.sort.bam
And the output was this:

Can't open perl script "/home/juaguila/miniconda3/envs/craq/bin/../src/fetch_size.pl": No such file or directory
Running CRAQ analysis .........
PARAMETERS:
Genome sequence(-g): myse-hapog.fasta
SMS input(-sms):
NGS input(-ngs): MYSE.Q20.mapped.sort.bam
Minimum NGS clipped-reads (-sn): 2
Minimum SMS clipped-reads (-ln): 2
Clipping coverRate(-sf): 0.75
Lower clipping rate for heterozygous allele(-hmin): 0.4
Upper clipping rate for heterozygous allele(-hmax): 0.6
Block score benchmarking (-rw): 1000000
Gap[N] is treated with (-gm): 1:CRE
Minimum gapsize(-mgs): 10
Break chimera fragments (-b): F
Search error region (-ser): T
Mapping SMS reads use (-x): map-hifi
Mapping quality (-q): 20
Can't open perl script "/home/juaguila/miniconda3/envs/craq/bin/../src/compute_norm_window.pl": No such file or directory
Window size for error normalizing (-nw):
Plot CRAQ metrics (-pl): F
Alignment thread(-t): 10
Current working at : /DataDrive/juaguila/MYSE-PESU/MYSE
CRAQ output dir(-D): /DataDrive/juaguila/MYSE-PESU/MYSE/output
-------------------------Start Running-------------------------
Running NGS short-reads CRAQ analysis ......
CMD: /home/juaguila/miniconda3/envs/craq/bin/../src/runSR.sh -g myse-hapog.fasta -z seq.size -1 MYSE.Q20.mapped.sort.bam -q 20 -m 2 -f 0.4 -h 0.6 -r 0.75 -a 100 -t 10
bash: /home/juaguila/miniconda3/envs/craq/bin/../src/runSR.sh: No such file or directory

Running CRAQ benchmark analysis ......
CMD: /home/juaguila/miniconda3/envs/craq/bin/../src/runAQI_NGS.sh -g myse-hapog.fasta -z seq.size -e SRout/SR_eff.size -c SRout/SR_putative.RE.RH -d SRout/SR_sort.depth -r 0.75 -p 0.4 -q 0.6 -n 10 -s -w 1000000 -j 1 -u T -v F -y F -x /DataDrive/juaguila/MYSE-PESU/MYSE/output/seq.size
bash: /home/juaguila/miniconda3/envs/craq/bin/../src/runAQI_NGS.sh: No such file or directory

[JiaoLaboratory]

This is not realiable, I haven't meet this problem yet, try using "git clone https://github.com/JiaoLaboratory/CRAQ.git" or "wget https://github.com/JiaoLaboratory/CRAQ/archive/ refs/heads/main.zip"; then runing: "perl CRAQ-main/bin/craq -h " to test

[chenys1998]

I met this error too. When i install CRAQ by conda, it can not find all scripts in $you_conda_envs/bin/../src/*.
Actually, conda put all script in $you_conda_envs/share/CRAQ/sra/，(if not, you can find this by find $you_conda_envs -name fetch_size.pl).
And then you can link this file to $you_conda_envs/src, this error can be solved.