search

maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
Other
68 stars 43 forks source link

KeyError: 'lindel' #32

Closed tiramisutes closed 4 years ago

tiramisutes commented 4 years ago

Dear, I get the follows stderr when running crisporWebsite for Cpf1 in the command line. This is my command 

python crispor.py genome A01G000010.1.fa /public/home/software/crisporWebsite/genome.mine.tab -o /public/home/software/crisporWebsite/genome.Offtargets.mine.tab -g  -p TTTN

The stderr messages:

INFO:root: * running on sequence 'A01G000010.1.exon1', guideLen=23, seqLen=1432
INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - bwasw - Searching genome for one 100% identical match to input sequence
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (1432 bp) ...
[main] Version: 0.7.15-r1140
[main] CMD: /public/home/software/crisporWebsite/bin/Linux/bwa bwasw -T 20 /public/home/CRISPR/genome.fa /tmp/crisporBestMatch2gfVeQ.fa
[main] Real time: 10.055 sec; CPU: 3.776 sec
INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - effScores - Calculating guide efficiency scores
Using Theano backend.
INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - outcome - Calculating editing outcomes
Traceback (most recent call last):
  File "crispor.py", line 8293, in <module>
    main()
  File "crispor.py", line 8291, in main
    mainCommandLine()
  File "crispor.py", line 8100, in mainCommandLine
    getOfftargets(seq, org, pamPat, batchId, startDict, ConsQueue())
  File "crispor.py", line 4295, in getOfftargets
    processSubmission(faFname, org, pamDesc, otBedFname, batchBase, batchId, queue)
  File "crispor.py", line 3835, in processSubmission
    createBatchEffScoreTable(batchId, queue)
  File "crispor.py", line 3454, in createBatchEffScoreTable
    guideRows = calcSaveEffScores(batchId, seq, extSeq, pam, queue)
  File "crispor.py", line 3401, in calcSaveEffScores
    effScores[mutScoreName] = extractMutScores(mutScores[mutScoreName], pamIds)
KeyError: 'lindel'

Any help is much appreciated. Thanks.

Best regards,

maximilianh commented 4 years ago

I’ll have to look into it later but for now you could simply remove lindel somewhere at the top of crispor.py there is a list of scoring models that are active.

On Sun 7 Jul 2019 at 04:55, hope notifications@github.com wrote:

Dear, I get the follows stderr when running crisporWebsite in command line. This is my command

python crispor.py genome A01G000010.1.fa /public/home/software/crisporWebsite/genome.mine.tab -o /pub lic/home/software/crisporWebsite/genome.Offtargets.mine.tab -g -p TTTN

The stderr messages:

INFO:root: * running on sequence 'A01G000010.1.exon1', guideLen=23, seqLen=1432 INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - bwasw - Searching genome for one 100% identical match to input sequence [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 1 sequences/pairs (1432 bp) ... [main] Version: 0.7.15-r1140 [main] CMD: /public/home/software/crisporWebsite/bin/Linux/bwa bwasw -T 20 /public/home/CRISPR/TM-1/genome.fa /tmp/crisporBestMatch2gfVeQ.fa [main] Real time: 10.055 sec; CPU: 3.776 sec INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - effScores - Calculating guide efficiency scores Using Theano backend. INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - outcome - Calculating editing outcomes Traceback (most recent call last): File "crispor.py", line 8293, in main() File "crispor.py", line 8291, in main mainCommandLine() File "crispor.py", line 8100, in mainCommandLine getOfftargets(seq, org, pamPat, batchId, startDict, ConsQueue()) File "crispor.py", line 4295, in getOfftargets processSubmission(faFname, org, pamDesc, otBedFname, batchBase, batchId, queue) File "crispor.py", line 3835, in processSubmission createBatchEffScoreTable(batchId, queue) File "crispor.py", line 3454, in createBatchEffScoreTable guideRows = calcSaveEffScores(batchId, seq, extSeq, pam, queue) File "crispor.py", line 3401, in calcSaveEffScores effScores[mutScoreName] = extractMutScores(mutScores[mutScoreName], pamIds) KeyError: 'lindel'

Any help is much appreciated. Thanks.

Best regards,

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/crisporWebsite/issues/32?email_source=notifications&email_token=AACL4TJHOKAW3WCIGOSIIMLP6HKUFA5CNFSM4H6VQGE2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G5WPZ4A, or mute the thread https://github.com/notifications/unsubscribe-auth/AACL4TLX6HJR62TEWXNFEYLP6HKUFANCNFSM4H6VQGEQ .

tiramisutes commented 4 years ago

I’ll have to look into it later but for now you could simply remove lindel somewhere at the top of crispor.py there is a list of scoring models that are active. … On Sun 7 Jul 2019 at 04:55, hope @.**> wrote: Dear, I get the follows stderr when running crisporWebsite in command line. This is my command python crispor.py genome A01G000010.1.fa /public/home/software/crisporWebsite/genome.mine.tab -o /pub lic/home/software/crisporWebsite/genome.Offtargets.mine.tab -g -p TTTN The stderr messages: INFO:root: running on sequence 'A01G000010.1.exon1', guideLen=23, seqLen=1432 INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - bwasw - Searching genome for one 100% identical match to input sequence [M::bwa_idx_load_from_disk] read 0 ALT contigs [bsw2_aln] read 1 sequences/pairs (1432 bp) ... [main] Version: 0.7.15-r1140 [main] CMD: /public/home/software/crisporWebsite/bin/Linux/bwa bwasw -T 20 /public/home/CRISPR/TM-1/genome.fa /tmp/crisporBestMatch2gfVeQ.fa [main] Real time: 10.055 sec; CPU: 3.776 sec INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - effScores - Calculating guide efficiency scores Using Theano backend. INFO:root:Progress sB5Xn3UxqFPZmXaCAlYP - outcome - Calculating editing outcomes Traceback (most recent call last): File "crispor.py", line 8293, in main() File "crispor.py", line 8291, in main mainCommandLine() File "crispor.py", line 8100, in mainCommandLine getOfftargets(seq, org, pamPat, batchId, startDict, ConsQueue()) File "crispor.py", line 4295, in getOfftargets processSubmission(faFname, org, pamDesc, otBedFname, batchBase, batchId, queue) File "crispor.py", line 3835, in processSubmission createBatchEffScoreTable(batchId, queue) File "crispor.py", line 3454, in createBatchEffScoreTable guideRows = calcSaveEffScores(batchId, seq, extSeq, pam, queue) File "crispor.py", line 3401, in calcSaveEffScores effScores[mutScoreName] = extractMutScores(mutScores[mutScoreName], pamIds) KeyError: 'lindel' Any help is much appreciated. Thanks. Best regards, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#32?email_source=notifications&email_token=AACL4TJHOKAW3WCIGOSIIMLP6HKUFA5CNFSM4H6VQGE2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G5WPZ4A>, or mute the thread https://github.com/notifications/unsubscribe-auth/AACL4TLX6HJR62TEWXNFEYLP6HKUFANCNFSM4H6VQGEQ .

Thanks for your reply. Let me try.

maximilianh commented 4 years ago

I think this problem is solved now. Lindel doesn't work with Cpf1 and there was a bug for a while where it wasn't properly removed from the list of models.