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maximilianh / crisporWebsite

All source code of the crispor.org website
http://crispor.org
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File "../bin/samToBed", line 14, in <module> IndexError: list index out of range #9

Closed elijahlowe closed 6 years ago

elijahlowe commented 6 years ago

I am receiving the following area and can not figure out the problem. I'm running the cold on the test data.

../crispor.cgi sacCer3 sampleIn.fa sampleOut.mine.tsv -o sampleOutOfftargets.mine.tsv
INFO:root:running on sequence ID 'testSeq'
[bsw2_aln] read 1 sequences/pairs (182 bp) ...
[main] Version: 0.7.9a-r786
[main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa bwasw -T 20 /Users/elowe3/bioinformatics_software/crisporWebsite/genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crisporBestMatchT56QC_.fa
[main] Real time: 0.022 sec; CPU: 0.020 sec
INFO:root:Progress x50sPGMoTvUagv3zWjGg - effScores - Calculating guide efficiency scores
INFO:root:Wrote eff scores to /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.effScores.tab
INFO:root:Progress x50sPGMoTvUagv3zWjGg - bwa - Alignment of potential guides, mismatches <= 4
[bwa_aln_core] calculate SA coordinate... 0.08 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.9a-r786
[main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa aln -o 0 -m 1980000 -n 4 -k 4 -N -l 20 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa
[main] Real time: 0.122 sec; CPU: 0.116 sec
INFO:root:Progress x50sPGMoTvUagv3zWjGg - saiToBed - Converting alignments
[bwa_aln_core] convert to sequence coordinate... 0.01 sec
[bwa_aln_core] refine gapped alignments... 0.00 sec
[bwa_aln_core] print alignments... 0.00 sec
[bwa_aln_core] 7 sequences have been processed.
[main] Version: 0.7.9a-r786
[main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa samse -n 60000 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.sa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa
[main] Real time: 0.047 sec; CPU: 0.046 sec
Traceback (most recent call last):
  File "../bin/samToBed", line 14, in <module>
    guideLen = int(sys.argv[2])
IndexError: list index out of range
ERROR:root:Error: could not run command set -o pipefail; /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa samse -n 60000 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.sa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa | ../bin/xa2multi.pl | ../bin/samToBed NGG | sort -k1,1 -k2,2n | /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bedClip stdin ../genomes/sacCer3/sacCer3.sizes stdout >> /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.matches.bed .
maximilianh commented 6 years ago

Wow, this is strange! Are you really sure that you checked out the master branch? I tried it with the current master branch and samToBed needs the additional argument "20" now to work. In the current master branch, it's "samToBed NGG 20", not "samToBed NGG". Are you using an old version?

I made this change half a year ago or so. I don't know how you downloaded such an old version of the software.

On Wed, Mar 7, 2018 at 6:44 PM, Elijah Lowe notifications@github.com wrote:

I am receiving the following area and can not figure out the problem. I'm running the cold on the test data.

../crispor.cgi sacCer3 sampleIn.fa sampleOut.mine.tsv -o sampleOutOfftargets.mine.tsv INFO:root:running on sequence ID 'testSeq' [bsw2_aln] read 1 sequences/pairs (182 bp) ... [main] Version: 0.7.9a-r786 [main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa bwasw -T 20 /Users/elowe3/bioinformaticssoftware/crisporWebsite/genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crisporBestMatchT56QC.fa [main] Real time: 0.022 sec; CPU: 0.020 sec INFO:root:Progress x50sPGMoTvUagv3zWjGg - effScores - Calculating guide efficiency scores INFO:root:Wrote eff scores to /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.effScores.tab INFO:root:Progress x50sPGMoTvUagv3zWjGg - bwa - Alignment of potential guides, mismatches <= 4 [bwa_aln_core] calculate SA coordinate... 0.08 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.9a-r786 [main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa aln -o 0 -m 1980000 -n 4 -k 4 -N -l 20 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa [main] Real time: 0.122 sec; CPU: 0.116 sec INFO:root:Progress x50sPGMoTvUagv3zWjGg - saiToBed - Converting alignments [bwa_aln_core] convert to sequence coordinate... 0.01 sec [bwa_aln_core] refine gapped alignments... 0.00 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 7 sequences have been processed. [main] Version: 0.7.9a-r786 [main] CMD: /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa samse -n 60000 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.sa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa [main] Real time: 0.047 sec; CPU: 0.046 sec Traceback (most recent call last): File "../bin/samToBed", line 14, in guideLen = int(sys.argv[2]) IndexError: list index out of range ERROR:root:Error: could not run command set -o pipefail; /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bwa samse -n 60000 ../genomes/sacCer3/sacCer3.fa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.sa /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.fa | ../bin/xa2multi.pl | ../bin/samToBed NGG | sort -k1,1 -k2,2n | /Users/elowe3/bioinformatics_software/crisporWebsite/bin/Darwin/bedClip stdin ../genomes/sacCer3/sacCer3.sizes stdout >> /var/folders/bz/lbll3mbn29v8bpf5w2hfdfyngydffc/T/crispormG6saZ/x50sPGMoTvUagv3zWjGg.matches.bed .

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elijahlowe commented 6 years ago

I got the same error, I even check to make sure I had the correct branch:

git checkout master
M   bin/Darwin/WU-CRISPR/result/sgOligo_V0.9_prediction_result.xls
D   genomes.sample/sacCer3/genomeInfo.tab
D   genomes.sample/sacCer3/sacCer3.2bit
D   genomes.sample/sacCer3/sacCer3.fa.amb
D   genomes.sample/sacCer3/sacCer3.fa.ann
D   genomes.sample/sacCer3/sacCer3.fa.bwt
D   genomes.sample/sacCer3/sacCer3.fa.pac
D   genomes.sample/sacCer3/sacCer3.fa.sa
D   genomes.sample/sacCer3/sacCer3.segments.bed
D   genomes.sample/sacCer3/sacCer3.sizes
Already on 'master'
Your branch is up-to-date with 'origin/master'.

after that I deleted the repo and cloned it again but to no avail.

maximilianh commented 6 years ago

How about this command? Does this show the same line? Especially this part: "$SCRIPT/samToBed %(pam)s %(seqLen)d"

$ grep "samToBed" crispor.py

cmd = "$BIN/bwa samse -n %(maxOcc)d

%(genomeDir)s/%(genome)s/%(genome)s.fa %(saFname)s %(faFname)s | $SCRIPT/xa2multi.pl | $SCRIPT/samToBed %(pam)s %(seqLen)d | sort -k1,1 -k2,2n | $BIN/bedClip stdin %(genomeDir)s/%(genome)s/%(genome)s.sizes stdout >> %(matchesBedFname)s " % locals()

in my master branch, this is the file size: $ ls -la crispor.py

-rwxrwxr-x 1 max max 291440 Mar 6 07:16 crispor.py

You're not on a fork, are you?

$ git remote -v

origin git@github.com:maximilianh/crisporWebsite.git (fetch)

$ git status crispor.py On branch master Your branch is up-to-date with 'origin/master'.

nothing to commit, working directory clean

On Thu, Mar 8, 2018 at 2:52 PM, Elijah Lowe notifications@github.com wrote:

I got the same error, I even check to make sure I had the correct branch:

git checkout master M bin/Darwin/WU-CRISPR/result/sgOligo_V0.9_prediction_result.xls D genomes.sample/sacCer3/genomeInfo.tab D genomes.sample/sacCer3/sacCer3.2bit D genomes.sample/sacCer3/sacCer3.fa.amb D genomes.sample/sacCer3/sacCer3.fa.ann D genomes.sample/sacCer3/sacCer3.fa.bwt D genomes.sample/sacCer3/sacCer3.fa.pac D genomes.sample/sacCer3/sacCer3.fa.sa D genomes.sample/sacCer3/sacCer3.segments.bed D genomes.sample/sacCer3/sacCer3.sizes Already on 'master' Your branch is up-to-date with 'origin/master'.

after that I deleted the repo and cloned it again but to no avail.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

elijahlowe commented 6 years ago

All of them are the same, the output from grep:

grep "samToBed" crispor.py
cmd = "$BIN/bwa samse -n %(maxOcc)d %(genomeDir)s/%(genome)s/%(genome)s.fa %(saFname)s %(faFname)s | $SCRIPT/xa2multi.pl | $SCRIPT/samToBed %(pam)s %(seqLen)d | sort -k1,1 -k2,2n | $BIN/bedClip stdin %(genomeDir)s/%(genome)s/%(genome)s.sizes stdout >> %(matchesBedFname)s " % locals()

The file size:

ls -la crispor.py
-rwxr-xr-x  1 elowe3  AD\Domain Users  291440 Mar  8 09:21 crispor.py

And the branch:

git remote -v
origin  https://github.com/maximilianh/crisporWebsite.git (fetch)
origin  https://github.com/maximilianh/crisporWebsite.git (push)

git status crispor.py
On branch master
Your branch is up-to-date with 'origin/master'.

nothing to commit, working tree clean
maximilianh commented 6 years ago

Oh wow, I'm erm... not tidy. Please replace "crispor.cgi" in the command with "crispor.py" ? Apparently I still have a super old version of the script in the repo! How weird that I've never seen it and no one else ever pointed it out. Sorry! I'll clean up my repo now and fix the docs.

many thanks for pointing this out!

elijahlowe commented 6 years ago

yup, that did it. I'm surprised I didn't catch it myself. Thanks for the help.