search

maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
Other
72 stars 42 forks source link

bwa errors during local installtion #69

Open ranelmalka100 opened 3 months ago

ranelmalka100 commented 3 months ago

Hello :)

I'm trying to locally install crispor, I've started by installing all the required packages according to the requirments.txt file, and it ended successfully :)

Next, I tried to run crispor.py script, using one of my desired sequences as example, as mentioned here - python ../crispor.py h38 ../ENST00000009589.8.fasta exampleout.tsv. I also followed the instructions in 'Adding a genome'.

I've got these messages and error -

INFO:root: * running on sequence 'ENST00000009589.8', guideLen=20, seqLen=519 INFO:root:Progress G0QukS5zrvfbiD5rGwRh - bwasw - Searching genome for one 100% identical match to input sequence [E::bwa_idx_load_from_disk] fail to locate the index files ERROR:root:Error: could not run command set -o pipefail; true G0QukS5zrvfbiD5rGwRh noIp&&/aldemaslab/nofar/crisporWebsite/bin/Linux/bwa bwasw -b 100 -q 100 -T 20 /aldemasla b/nofar/crisporWebsite/genomes/h38/h38.fa /var/tmp/primer3Inmd623rvl.txt > /var/tmp/primer3In78bghbla.txt.

I manually downloaded all the index files of the human genome from the proposed link, and tried to run the script, but still got the same error.

Can you please help and explain me what am I doing wrong ><

Thanks in advance, Nofar :-]

maximilianh commented 3 months ago

Hi, you're not doing anything wrong, the website moved to python3 and it's well possible that something is difficult now with the installation.

Did you check that bwa is working on your machine? Can you run the program /aldemaslab/nofar/crisporWebsite/bin/Linux/bwa ?

On Wed, Aug 7, 2024 at 11:05 AM ranelmalka100 @.***> wrote:

Hello :)

I'm trying to locally install crispor, I've started by installing all the required packages according to the requirments.txt file, and it ended successfully :)

Next, I tried to run crispor.py script, using one of my desired sequences as example, as mentioned here - python ../crispor.py h38 ../ENST00000009589.8.fasta exampleout.tsv. I also followed the instructions in 'Adding a genome'.

I've got these messages and error - INFO:root: * running on sequence 'ENST00000009589.8', guideLen=20, seqLen=519 INFO:root:Progress G0QukS5zrvfbiD5rGwRh - bwasw - Searching genome for one 100% identical match to input sequence [E::bwa_idx_load_from_disk] fail to locate the index files ERROR:root:Error: could not run command set -o pipefail; true G0QukS5zrvfbiD5rGwRh noIp&&/aldemaslab/nofar/crisporWebsite/bin/Linux/bwa bwasw -b 100 -q 100 -T 20 /aldemasla b/nofar/crisporWebsite/genomes/h38/h38.fa /var/tmp/primer3Inmd623rvl.txt > /var/tmp/primer3In78bghbla.txt.

I manually downloaded all the index files of the human genome from [ http://crispor.gi.ucsc.edu/genomes/hg38/], and tried to run the script, but still got the same error.

Can you please help and explain me what am I doing wrong ><

Thanks in advanve, Nofar :-]

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/crisporWebsite/issues/69, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TJ4ANR4CU43JBRWIT3ZQHPMNAVCNFSM6AAAAABMD6TKS6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2TEOJWGM4TAMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

ranelmalka100 commented 3 months ago

Thank you for the quick reply! bwa is indeed working on the machine. Is there anything else you would recommend to test?

maximilianh commented 3 months ago

you could run it with -d and see what that shows?

With -d the temp files are not removed, so then you can run the command shown from the command line without the "> xxx" at the end and see yourself what the command results are and why it's erroring out.

On Wed, Aug 7, 2024 at 2:29 PM ranelmalka100 @.***> wrote:

Thank you for the quick reply! bwa is indeed working on the machine. Is there anything else you would recommend to test?

— Reply to this email directly, view it on GitHub https://github.com/maximilianh/crisporWebsite/issues/69#issuecomment-2273357100, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TKGEQ32OW2IOJCHG33ZQIHKPAVCNFSM6AAAAABMD6TKS6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGM2TOMJQGA . You are receiving this because you commented.Message ID: @.***>

ranelmalka100 commented 3 months ago

After adding the the -d flag as you suggested, the command

 set -o pipefail; true G0QukS5zrvfbiD5rGwRh noIp&&/aldemaslab/nofar/crisporWebsite/bin/Linux/bwa bwasw -d -b 100 -q 100 -T 20 /aldemasla b/nofar/crisporWebsite/genomes/h38/h38.fa /var/tmp/primer3Inmd623rvl.txt

Ended successfully.

ranelmalka100 commented 3 months ago

I just found out that the error was a typo in the first command. Instead of hg38 I wrote h38. After fixing the typo the code ran successfully. Thank you very much for the quick replies and helpful support! :-]