search

pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Other
278 stars 95 forks source link

ERROR: Cannot set a frame with no defined index and a value that cannot be converted to a Series #176

Closed deb0612 closed 1 year ago

deb0612 commented 3 years ago

Dear sir, When I tried to use : "CRISPRessoWGS -b 1K/PCR-KL20211111-ALAS1-1_S52_L002.sorted.bam.bam -f guide.txt -r ALAS1_ngs1k.fasta" It shows massage like


                -Analysis of CRISPR/Cas9 outcomes from WGS data-

                  _                                            _
                 '  )                                         '  )
                 .-'              ____________                .-'
                (____            |     __  __ |              (____
             C)|     \           ||  |/ _ (_  |           C)|     \
               \     /           ||/\|\__)__) |             \     /
                \___/            |____________|              \___/

                          [CRISPResso version 2.0.40]
                    [Kendell Clement and Luca Pinello 2020]
                 [For support contact kclement@mgh.harvard.edu]

INFO  @ Thu, 25 Nov 2021 14:54:15:
         Checking dependencies...

INFO  @ Thu, 25 Nov 2021 14:54:15:

 All the required dependencies are present!

INFO  @ Thu, 25 Nov 2021 14:54:15:
         Creating Folder CRISPRessoWGS_on_PCR-KL20211111-ALAS1-1_S52_L002.sorted

WARNING @ Thu, 25 Nov 2021 14:54:15:
         Folder CRISPRessoWGS_on_PCR-KL20211111-ALAS1-1_S52_L002.sorted already exists.

INFO  @ Thu, 25 Nov 2021 14:54:15:
         Index file for input .bam file exists, skipping generation.

INFO  @ Thu, 25 Nov 2021 14:54:15:
         The index for the reference fasta file is already present! Skipping generation.

INFO  @ Thu, 25 Nov 2021 14:54:15:
         Retrieving reference sequences for amplicons and checking for sgRNAs

CRITICAL @ Thu, 25 Nov 2021 14:54:15:

ERROR: Cannot set a frame with no defined index and a value that cannot be converted to a Series

My reference was indexed by bowtie2. How could I improve them?
[guide.txt](https://github.com/pinellolab/CRISPResso2/files/7600861/guide.txt)
[ALAS1_ngs1k.fasta.txt](https://github.com/pinellolab/CRISPResso2/files/7600877/ALAS1_ngs1k.fasta.txt)
kclem commented 2 years ago

Hi @deb0612 I haven't seen this problem. If you update to a more recent version do you get this same error?

Colelyman commented 2 years ago

Also, if the error persists could you provide the output with the --debug parameter added?

kclem commented 1 year ago

We're closing this issue because it hasn't been updated recently. If this issue still exists, please reopen this issue and we'll look into it!